Mm10 conservation alignment: Difference between revisions
From genomewiki
Jump to navigationJump to search
(updated data) |
(updated data) |
||
| Line 240: | Line 240: | ||
<TD ALIGN=RIGHT>2009-09-02</TD> | <TD ALIGN=RIGHT>2009-09-02</TD> | ||
<TD ALIGN=RIGHT>N/A</TD> | <TD ALIGN=RIGHT>N/A</TD> | ||
<TD> | <TD>2012-03-23</TD><TD ALIGN=RIGHT>17.004%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[http://www.ncbi.nlm.nih.gov/genome/614 32]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=myoLuc2 myoLuc2]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABVD00 Myotis<BR>lucifugus]</TD><TD>Microbat</TD> | <TH>[http://www.ncbi.nlm.nih.gov/genome/614 32]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=myoLuc2 myoLuc2]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABVD00 Myotis<BR>lucifugus]</TD><TD>Microbat</TD> | ||
| Line 268: | Line 268: | ||
<TD ALIGN=RIGHT>2009-09-02</TD> | <TD ALIGN=RIGHT>2009-09-02</TD> | ||
<TD ALIGN=RIGHT>N/A</TD> | <TD ALIGN=RIGHT>N/A</TD> | ||
<TD> | <TD>2012-03-23</TD><TD ALIGN=RIGHT>15.147%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[http://www.ncbi.nlm.nih.gov/genome/771 36]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ochPri2 ochPri2]</TH><TD>[http://www.ncbi.nlm.nih.gov/bioproject/74593 Ochotona<BR>princeps]</TD><TD>Pika</TD> | <TH>[http://www.ncbi.nlm.nih.gov/genome/771 36]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ochPri2 ochPri2]</TH><TD>[http://www.ncbi.nlm.nih.gov/bioproject/74593 Ochotona<BR>princeps]</TD><TD>Pika</TD> | ||
| Line 275: | Line 275: | ||
<TD ALIGN=RIGHT>2009-09-02</TD> | <TD ALIGN=RIGHT>2009-09-02</TD> | ||
<TD ALIGN=RIGHT>N/A</TD> | <TD ALIGN=RIGHT>N/A</TD> | ||
<TD> | <TD>2012-03-24</TD><TD ALIGN=RIGHT>N/A</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/hedgehog/eriEur1/ 37]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=eriEur1 eriEur1]</TH><TD>[http://www.ncbi.nlm.nih.gov/genome/227 Erinaceus<BR>europaeus]</TD><TD>Hedgehog</TD> | <TH>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/hedgehog/eriEur1/ 37]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=eriEur1 eriEur1]</TH><TD>[http://www.ncbi.nlm.nih.gov/genome/227 Erinaceus<BR>europaeus]</TD><TD>Hedgehog</TD> | ||
| Line 282: | Line 282: | ||
<TD ALIGN=RIGHT>2009-09-02</TD> | <TD ALIGN=RIGHT>2009-09-02</TD> | ||
<TD ALIGN=RIGHT>2009-09-02</TD> | <TD ALIGN=RIGHT>2009-09-02</TD> | ||
<TD> | <TD>2012-03-24</TD><TD ALIGN=RIGHT>9.856%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/tenrec/echTel1/ 38]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=echTel1 echTel1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAIY00 Echinops<BR>telfairi]</TD><TD>Tenrec</TD> | <TH>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/tenrec/echTel1/ 38]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=echTel1 echTel1]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAIY00 Echinops<BR>telfairi]</TD><TD>Tenrec</TD> | ||
| Line 289: | Line 289: | ||
<TD ALIGN=RIGHT>2009-09-02</TD> | <TD ALIGN=RIGHT>2009-09-02</TD> | ||
<TD ALIGN=RIGHT>N/A</TD> | <TD ALIGN=RIGHT>N/A</TD> | ||
<TD> | <TD>2012-03-24</TD><TD ALIGN=RIGHT>10.947%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/commonShrew/sorAra1/ 39]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=sorAra1 sorAra1]</TH><TD>[http://www.ncbi.nlm.nih.gov/genome/91 Sorex<BR>araneus]</TD><TD>Shrew</TD> | <TH>[ftp://ftp.broad.mit.edu/pub/assemblies/mammals/commonShrew/sorAra1/ 39]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=sorAra1 sorAra1]</TH><TD>[http://www.ncbi.nlm.nih.gov/genome/91 Sorex<BR>araneus]</TD><TD>Shrew</TD> | ||
| Line 296: | Line 296: | ||
<TD ALIGN=RIGHT>2009-09-02</TD> | <TD ALIGN=RIGHT>2009-09-02</TD> | ||
<TD ALIGN=RIGHT>2009-09-02</TD> | <TD ALIGN=RIGHT>2009-09-02</TD> | ||
<TD> | <TD>2012-03-24</TD><TD ALIGN=RIGHT>9.382%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[http://www.ncbi.nlm.nih.gov/genome/233 40]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=macEug2 macEug2]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABQO00 Macropus<BR>eugenii]</TD><TD>Wallaby</TD> | <TH>[http://www.ncbi.nlm.nih.gov/genome/233 40]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=macEug2 macEug2]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ABQO00 Macropus<BR>eugenii]</TD><TD>Wallaby</TD> | ||
| Line 303: | Line 303: | ||
<TD ALIGN=RIGHT>2010-11-05</TD> | <TD ALIGN=RIGHT>2010-11-05</TD> | ||
<TD ALIGN=RIGHT>2011-12-02</TD> | <TD ALIGN=RIGHT>2011-12-02</TD> | ||
<TD> | <TD>2012-03-24</TD><TD ALIGN=RIGHT>4.353%</TD> | ||
</TR><TR> | </TR><TR> | ||
<TH>[http://www.broadinstitute.org/mammals/opossum 41]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=monDom5 monDom5]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAFR03 Monodelphis<BR>domestica]</TD><TD>Opossum</TD> | <TH>[http://www.broadinstitute.org/mammals/opossum 41]</TH><TH>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=monDom5 monDom5]</TH><TD>[http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAFR03 Monodelphis<BR>domestica]</TD><TD>Opossum</TD> | ||
Revision as of 17:02, 26 March 2012
see also
- Mouse 60-way Mm10 Genome size statistics
- Mouse 60-way Mm10 conservation lastz parameters
- all other UCSC Multiple Alignments
do not edit
This table is automatically generated off-line from the UCSC databases. Please do not edit it.
| URL to assembly sequence |
UCSC db name/ genome-preview browser |
Scientific name/ assembly information |
Common name |
assembly date | source version |
Repeat Masker |
Window Masker |
chain on mm10 |
% of mm10 matched (chainLink table) |
|---|---|---|---|---|---|---|---|---|---|
| 01 | mm10 | Mus musculus | Mouse | Dec. 2011 (GRCm38/mm10) | Genome Reference Consortium Mouse Build 38 (GCA_000001635.2) | 2012-02-06 | 2012-02-07 | N/A | N/A |
| 02 | rn4 | Rattus norvegicus | Rat | Nov. 2004 (Baylor 3.4/rn4) | Baylor HGSC v. 3.4 | 2009-08-15 | N/A | 2012-03-08 | 54.645% |
| 03 | speTri2 | Spermophilus tridecemlineatus | Squirrel | Nov. 2011 (Broad SpeTri2/speTri2) | Broad Institute (GCA_000236235.1) | 2012-03-14 | 2012-03-15 | 2012-03-16 | 34.217% |
| 04 | micMur1 | Microcebus murinus | Mouse lemur | Jun. 2003 (Broad/micMur1) | Broad Institute micMur1 (NCBI project 19967, ABDC00000000) | 2009-09-02 | N/A | 2012-03-13 | 26.636% |
| 05 | dipOrd1 | Dipodomys ordii | Kangaroo rat | Jul. 2008 (Broad/dipOrd1) | Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000) | 2009-09-02 | N/A | 2012-03-16 | 19.460% |
| 06 | saiBol1 | Saimiri boliviensis | Squirrel monkey | Oct. 2011 (SaiBol1.0/saiBol1) | Broad SaiBol1.0 (GCA_000235385.1) | 2012-01-07 | 2012-01-09 | 2012-03-09 | 32.339% |
| 07 | hetGla1 | Heterocephalus glaber | Naked mole-rat | Jul. 2011 (HetGla_1.0/hetGla1) | HetGla_1.0 (NCBI project 68323, accession GCA_000230455.1) | 2011-12-03 | 2011-12-06 | 2012-03-16 | 32.163% |
| 08 | hg19 | Homo sapiens | Human | Feb. 2009 (GRCh37/hg19) | GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1) | 2009-08-15 | N/A | 2012-03-08 | 38.226% |
| 09 | gorGor3 | Gorilla gorilla gorilla | Gorilla | May 2011 (gorGor3.1/gorGor3) | Wellcome Trust Sanger Institute May 2011 (NCBI project 31265, GCA_000151905.1) | 2011-11-16 | N/A | 2012-03-08 | 33.987% |
| 10 | panTro4 | Pan troglodytes | Chimp | Feb. 2011 (Pan_troglodytes-2.1.4/panTro4) | CSAC Pan_troglodytes-2.1.4 (GCA_000001515.4) | 2012-01-09 | 2012-01-09 | 2012-03-10 | 34.674% |
| 11 | nomLeu1 | Nomascus leucogenys | Gibbon | Jan. 2010 (GGSC Nleu1.0/nomLeu1) | GGSC (NCBI project 13975, accession GCA_000146795.1) | 2011-11-16 | N/A | 2012-03-08 | 34.132% |
| 12 | ponAbe2 | Pongo pygmaeus abelii | Orangutan | July 2007 (WUGSC 2.0.2/ponAbe2) | WUSTL 3.0 | 2009-08-15 | N/A | 2012-03-09 | 34.496% |
| 13 | tarSyr1 | Tarsius syrichta | Tarsier | Aug. 2008 (Broad/tarSyr1) | Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000) | 2009-09-02 | N/A | 2012-03-12 | 24.560% |
| 14 | rheMac3 | Macaca mulatta | Chinese rhesus | Oct. 2010 (BGI CR_1.0/rheMac3) | Beijing Genomics Institute, Shenzhen (GCA_000230795.1) | 2011-12-30 | 2012-01-03 | 2012-03-09 | 33.931% |
| 15 | papHam1 | Papio hamadryas | Baboon | Nov. 2008 (Baylor 1.0/papHam1) | Baylor BCM HGSC Pham_1.0 | 2009-09-02 | N/A | 2012-03-10 | 33.577% |
| 16 | otoGar3 | Otolemur garnettii | Bushbaby | Mar. 2011 (Broad OtoGar3/otoGar3) | Broad Institute (GCA_000181295.3) | 2012-03-13 | 2012-03-14 | 2012-03-13 | 29.795% |
| 17 | calJac3 | Callithrix jacchus | Marmoset | March 2009 (WUGSC 3.2/calJac3) | WUSTL 3.2 (GCA_000004665.1) | 2010-02-05 | N/A | 2012-03-09 | 32.450% |
| 18 | equCab2 | Equus caballus | Horse | Sep. 2007 (Broad/equCab2) | Broad Institute EquCab2 | 2009-08-14 | N/A | 2012-03-16 | 34.415% |
| 19 | cavPor3 | Cavia porcellus | Guinea pig | Feb. 2008 (Broad/cavPor3) | Broad Institute cavPor3 | 2009-08-15 | 2009-08-15 | 2012-03-17 | 28.447% |
| 20 | vicPac1 | Vicugna pacos | Alpaca | Jul. 2008 (Broad/vicPac1) | Broad Institute vicPac1 | 2009-09-02 | N/A | 2012-03-17 | 22.636% |
| 21 | turTru1 | Tursiops truncatus | Dolphin | Feb. 2008 (Broad/turTru1) | Broad Institute turTru1 (NCBI project 20367, ABRN01000000) | 2009-09-02 | N/A | 2012-03-17 | 28.761% |
| 22 | tupBel1 | Tupaia belangeri | Tree shrew | Dec. 2006 (Broad/tupBel1) | Broad Institute tupBel1 (NCBI project 13971, AAPY01000000) | 2009-09-02 | N/A | 2012-03-17 | 19.766% |
| 23 | susScr2 | Sus scrofa | Pig | Nov. 2009 (SGSC Sscrofa9.2/susScr2) | SGSC Sscrofa9.2 (NCBI project 10718, GCA_000003025.2) | 2010-03-25 | N/A | 2012-03-17 | 23.248% |
| 24 | oryCun2 | Oryctolagus cuniculus | Rabbit | Apr. 2009 (Broad/oryCun2) | Broad Institute oryCun2 (NCBI project 12819, AAGW00000000) | 2009-09-02 | N/A | 2012-03-17 | 25.248% |
| 25 | choHof1 | Choloepus hoffmanni | Sloth | Jul. 2008 (Broad/choHof1) | Broad Institute choHof1 | 2009-09-02 | N/A | 2012-03-22 | N/A |
| 26 | pteVam1 | Pteropus vampyrus | Megabat | Jul. 2008 (Broad/pteVam1) | Broad Institute pteVam1 (NCBI project 20325, ABRP01000000) | 2009-09-02 | N/A | 2012-03-20 | 27.345% |
| 27 | loxAfr3 | Loxodonta africana | Elephant | Jul. 2009 (Broad/loxAfr3) | Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000) | 2009-09-02 | N/A | 2012-03-20 | 25.823% |
| 28 | felCat4 | Felis catus | Cat | Dec. 2008 (NHGRI/GTB V17e/felCat4) | NHGRI/Genome Technology Branch (NCBI project 10703, accession ACBE0100000) | 2010-05-26 | N/A | 2012-03-20 | 24.033% |
| 29 | ailMel1 | Ailuropoda melanoleuca | Panda | Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) | BGI-Shenzhen AilMel 1.0 Dec. 2009 | 2010-02-03 | N/A | 2012-03-20 | 30.979% |
| 30 | canFam3 | Canis lupus familiaris | Dog | Sep. 2011 (Broad CanFam3.1/canFam3) | Broad CanFam3.1 (GCA_000002285.2) | 2012-01-05 | 2012-01-06 | 2012-03-20 | 29.144% |
| 31 | dasNov2 | Dasypus novemcinctus | Armadillo | Jul. 2008 (Broad/dasNov2) | Broad Institute dasNov2 (NCBI project 12594, AAGV020000000) | 2009-09-02 | N/A | 2012-03-23 | 17.004% |
| 32 | myoLuc2 | Myotis lucifugus | Microbat | Jul. 2010 (Broad Institute Myoluc2.0/myoLuc2) | Broad Institute (NCBI Project ID: 16951, Accession: GCA_000147115.1) | 2010-11-03 | N/A | 2012-03-22 | 24.363% |
| 33 | bosTau7 | Bos taurus | Cow | Oct. 2011 (Btau_4.6.1/bosTau7) | Btau_4.6.1 (NCBI project 12555, accession GCA_000003205.4) | 2012-01-04 | 2012-01-06 | 2012-03-22 | 26.255% |
| 34 | oviAri1 | Ovis aries | Sheep | Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) | ISGC (NCBI project 10709, accession GCA_000005525.1) | 2010-04-14 | N/A | 2012-03-22 | 15.341% |
| 35 | proCap1 | Procavia capensis | Rock hyrax | Jul. 2008 (Broad/proCap1) | Broad Institute proCap1 (NCBI project 13972, ABRQ01000000) | 2009-09-02 | N/A | 2012-03-23 | 15.147% |
| 36 | ochPri2 | Ochotona princeps | Pika | Jul. 2008 (Broad/ochPri2) | Broad Institute ochPri2 | 2009-09-02 | N/A | 2012-03-24 | N/A |
| 37 | eriEur1 | Erinaceus europaeus | Hedgehog | June 2006 (Broad/eriEur1) | Broad Institute eriEur1 (Draft_v1, NCBI project 12575) | 2009-09-02 | 2009-09-02 | 2012-03-24 | 9.856% |
| 38 | echTel1 | Echinops telfairi | Tenrec | July 2005 (Broad/echTel1) | Broad July 2005 | 2009-09-02 | N/A | 2012-03-24 | 10.947% |
| 39 | sorAra1 | Sorex araneus | Shrew | June 2006 (Broad/sorAra1) | Broad Institute sorAra1 (Draft_v2) | 2009-09-02 | 2009-09-02 | 2012-03-24 | 9.382% |
| 40 | macEug2 | Macropus eugenii | Wallaby | Sep. 2009 (TWGS Meug_1.1/macEug2) | TWGS (NCBI Project ID: 12586, Accession: GCA_000004035.1) | 2010-11-05 | 2011-12-02 | 2012-03-24 | 4.353% |
| 41 | monDom5 | Monodelphis domestica | Opossum | Oct. 2006 (Broad/monDom5) | Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000) | 2009-08-14 | 2009-08-14 | N/A | N/A |
| 42 | sarHar1 | Sarcophilus harrisii | Tasmanian devil | Feb. 2011 (WTSI Devil_ref v7.0/sarHar1) | Wellcome Trust Sanger Institute Devil_ref v7.0 (GCA_000189315.1) | 2012-02-02 | 2012-02-08 | N/A | N/A |
| [none 43] | ailMis1 | [none N/A] | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| [none 44] | croPor1 | [none N/A] | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 45 | ornAna1 | Ornithorhynchus anatinus | Platypus | Mar. 2007 (WUGSC 5.0.1/ornAna1) | WUSTL version 5.0.1 | 2009-08-15 | N/A | N/A | N/A |
| 46 | galGal4 | Gallus gallus | Chicken | Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) | ICGSC Gallus_gallus-4.0 (GCA_000002315.2) | 2012-01-04 | 2012-01-04 | N/A | N/A |
| 47 | taeGut1 | Taeniopygia guttata | Zebra finch | Jul. 2008 (WUGSC 3.2.4/taeGut1) | Washington University taeGut1 | 2009-08-14 | 2009-08-14 | N/A | N/A |
| 48 | melGal1 | Meleagris gallopavo | Turkey | Dec. 2009 (TGC Turkey_2.01/melGal1) | TGC (NCBI Project ID: 10805, Accession: GCA_000146605.1) | 2010-11-04 | N/A | N/A | N/A |
| 49 | chrPic1 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| 50 | anoCar2 | Anolis carolinensis | Lizard | May 2010 (Broad AnoCar2.0/anoCar2) | Broad Institute of MIT and Harvard AnoCar 2.0 (GCA_000090745.1) | 2011-04-12 | 2011-04-13 | N/A | N/A |
| 51 | xenTro3 | Xenopus tropicalis | X. tropicalis | Nov. 2009 (JGI 4.2/xenTro3) | US DOE Joint Genome Institute (JGI-PGF) (GCA_000004195.1) | 2011-09-08 | 2011-09-08 | N/A | N/A |
| 52 | latCha1 | Latimeria chalumnae | Coelacanth | Aug. 2011 (LatCha1/latCha1) | Broad LatCha1 (GCA_000225785.1) | 2012-01-11 | 2012-01-12 | N/A | N/A |
| 53 | gadMor1 | Gadus morhua | Atlantic cod | May. 2010 (Genofisk GadMor_May2010/gadMor1) | Genofisk GadMor_May2010 (GCA_000231765.1) | 2011-12-29 | 2012-01-04 | N/A | N/A |
| 54 | oreNil1 | Oreochromis niloticus | Nile tilapia | Jan. 2011 (Nile tilapia/oreNil1) | Broad Institute of MIT and Harvard Orenil1.0 (GCA_000188235.1) | 2011-11-30 | 2011-11-30 | N/A | N/A |
| 55 | gasAcu1 | Gasterosteus aculeatus | Stickleback | Feb. 2006 (Broad/gasAcu1) | Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000) | 2009-08-15 | 2009-08-15 | N/A | N/A |
| 56 | fr3 | Takifugu rubripes | Fugu | Oct. 2011 (FUGU5/fr3) | Fugu Genome Sequencing Consortium - FUGU5 (NCBI project 1434, GCA_000180615.2) | 2011-11-16 | 2011-11-17 | N/A | N/A |
| 57 | tetNig2 | Tetraodon nigroviridis | Tetraodon | Mar. 2007 (Genoscope 8.0/tetNig2) | Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000) | 2010-06-07 | 2009-09-02 | N/A | N/A |
| 58 | danRer7 | Danio rerio | Zebrafish | Jul. 2010 (Zv9/danRer7) | Wellcome Trust Sanger Institute Zv9 (GCA_000002035.2) | 2010-12-03 | N/A | N/A | N/A |
| 59 | oryLat2 | Oryzias latipes | Medaka | Oct. 2005 (NIG/UT MEDAKA1/oryLat2) | NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000) | 2009-08-15 | 2009-08-15 | N/A | N/A |
| 60 | petMar1 | Petromyzon marinus | Lamprey | Mar. 2007 (WUGSC 3.0/petMar1) | WUSTL v.3.0 (March 2007) | N/A | 2009-08-14 | N/A | N/A |
