Schema for TransMap RNA - TransMap GenBank RNA Mappings Version 5
  Database: hg38    Primary Table: transMapRnaV5 Data last updated: 2019-06-11
Big Bed File: /gbdb/hg38/transMap/V5/hg38.rna.transMapV5.bigPsl
Item Count: 981,052
Format description: bigPsl derived pairwise alignment with additional information
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166028719Start position in chromosome
chromEnd166028739End position in chromosome
namemm10:LF295859.1-10.1alignment Id
score588Score (0-1000), faction identity * 1000
strand++ or - indicates whether the query aligns to the + or - strand on the reference
thickStart166028739Start of where display should be thick (start codon)
thickEnd166028739End of where display should be thick (stop codon)
reserved0RGB value (use R,G,B string in input file)
blockCount2Number of blocks
blockSizes5,12,Comma separated list of block sizes
chromStarts0,8,Start positions relative to chromStart
oChromStart3Start position in other chromosome
oChromEnd20End position in other chromosome
oStrand++ or -, - means that psl was reversed into BED-compatible coordinates
oChromSize41Size of other chromosome.
oChromStarts3,8,Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand
oSequencegtatttgtgtgtgtgtgtgtgtgcgtgcgtgcgtgcgtgtcSequence on other chrom (or edit list, or empty)
oCDSCDS in NCBI format
chromSize248956422Size of target chromosome
match0Number of bases matched.
misMatch7 Number of bases that don't match
repMatch10 Number of bases that match but are part of repeats
nCount0 Number of 'N' bases
seqType10=empty, 1=nucleotide, 2=amino_acid
srcDbmm10source database
srcTransIdLF295859.1source transcript id
srcChromchr1source chromosome
srcChromStart167112859start position in source chromosome
srcChromEnd167120589end position in source chromosome
srcIdent1000source score (fraction identity * 1000)
srcAligned878fraction of source transcript aligned (fraction aligned * 1000)
geneNamegene name
geneIdgene id
geneTypeunknowngene type
transcriptTypeunknowntranscript type
chainTypesyntype of chains used for mapping
commonNameMousecommon name
scientificNameMus musculusscientific name
orgAbbrevMusorganism abbreviation

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsoChromStartoChromEndoStrandoChromSizeoChromStartsoSequenceoCDSchromSizematchmisMatchrepMatchnCountseqTypesrcDbsrcTransIdsrcChromsrcChromStartsrcChromEndsrcIdentsrcAlignedgeneNamegeneIdgeneTypetranscriptTypechainTypecommonNamescientificNameorgAbbrev
chr1166028719166028739mm10:LF295859.1-10.1588+166028739166028739025,12,0,8,320+413,8,gtatttgtgtgtgtgtgtgtgtgcgtgcgtgcgtgcgtgtc248956422071001mm10LF295859.1chr11671128591671205891000878unknownunknownsynMouseMus musculusMus
chr1166057619166059930musFur1:EZ504908.1-1.1795-16605993016605993001652,13,6,55,26,46,31,38,39,18,59,6,46,49,66,37,0,52,69,75,130,157,206,237,276,316,354,420,432,2159,2208,2274,0596+5960,53,66,74,130,156,202,235,273,312,330,389,395,441,492,559,attatacagcagaaaacccacttccatctttgaggcattcatccccagaatctgtcttcttggccccgtagagcacagtgagtgactcctctctgaagccacagataaaaggggggggggattctctc ...2489564224441202301musFur1EZ504908.1GL8969273611150361327510001000unknownunknownsynFerretMustela putorius furoMustel
chr1166057692166058017criGriChoV2:JI884885.1-1.1845-166058017166058017095,23,14,11,43,6,70,51,61,0,5,42,58,74,118,127,197,264,0287+2870,7,30,44,55,98,104,175,226,tttggaatacctcccttgcattggccccatctttaaaaataaaaataaaacaatttaaaaaggaaccagctaaattaatttaaacctcattgagaaatgtagcctatttttttcaccggccaccagcc ...248956422220442001criGriChoV2JI884885.1LT883665v1252613502526163710001000unknownunknownsynChinese hamsterCricetulus griseusCricet
chr1166057692166058017criGriChoV2:JP059969.1-1.1845-166058017166058017095,23,14,11,43,6,70,51,61,0,5,42,58,74,118,127,197,264,0287+2870,7,30,44,55,98,104,175,226,tttggaatacctcccttgcattggccccatctttaaaaataaaaataaaacaatttaaaaaggaaccagctaaattaatttaaacctcattgagaaatgtagcctatttttttcaccggccaccagcc ...248956422220442001criGriChoV2JP059969.1LT883665v1252613502526163710001000unknownunknownsynChinese hamsterCricetulus griseusCricet
chr1166058026166058596criGriChoV2:JI888996.1-1.1758-1660585961660585960144,41,23,3,19,3,43,157,42,12,54,37,32,31,0,5,49,75,78,97,100,144,302,348,391,470,507,539,0521+5210,4,45,68,77,97,104,147,304,346,358,412,457,490,tgaattccacagtagtgctccatgaagaatgctgtaatgtctaaaaactgttggatgtgttagagagtgtgtctgttgtatgcacaagagagtgctcccgcatagaaagagttcattttcccacccca ...24895642216412121601criGriChoV2JI888996.1LT883665v125261646252621661000998unknownunknownsynChinese hamsterCricetulus griseusCricet
chr1166058026166058596criGriChoV2:JP052281.1-1.1758-1660585961660585960144,41,23,3,19,3,43,157,42,12,54,37,32,31,0,5,49,75,78,97,100,144,302,348,391,470,507,539,0521+5210,4,45,68,77,97,104,147,304,346,358,412,457,490,tgaattccacagtagtgctccatgaagaatgctgtaatgtctaaaaactgttggatgtgttagagagtgtgtctgttgtatgcacaagagagtgctcccgcatagaaagagttcattttcccacccca ...24895642216412121601criGriChoV2JP052281.1LT883665v125261646252621661000998unknownunknownsynChinese hamsterCricetulus griseusCricet
chr1166059076166059324musFur1:EZ491718.1-1.1764-1660593241660593240635,68,38,61,31,1,0,41,112,150,216,247,0244+2440,35,103,143,204,243,gaatgagaactctcttcccacttctccagcccctcctcctcactctacccatctggtcaaccagcctgggtagatccccagagagttggcaggtctcagcattttgcacccccaaggctggtgcctgc ...24895642217955001musFur1EZ491718.1GL8969273612425361266910001000unknownunknownsynFerretMustela putorius furoMustel
chr1166059266166070537criGriChoV2:JI875801.1-1.1808-16607053716607053704129,17,20,40,10,5,44,13,8,36,18,23,39,28,17,12,22,10,49,87,45,15,35,17,165,9,26,17,22,38,54,30,43,41,30,7,70,74,47,398,306,0,30,52,77,119,129,134,178,197,205,244,262,285,325,354,371,384,410,420,469,557,602,618,653,670,841,869,895,914,936,975,1031,1063 ...02096+20960,29,46,66,106,121,146,191,204,217,253,272,296,335,363,386,398,420,431,482,569,615,630,666,700,865,874,913,930,954,992,1046,1076 ...aagagggaccaaagttttaccacctggctggtggccatgaacaccaccacaaaggagaagatcattctgcagaccatcaagtggaggatgagagtggacattgaagtggaccccctgcagctgttggg ...248956422143238619801criGriChoV2JI875801.1LT883665v125262842252733229991000unknownunknownsynChinese hamsterCricetulus griseusCricet
chr1166059266166070537criGriChoV2:JP051638.1-1.1808-16607053716607053704047,20,40,10,5,44,13,8,36,18,23,39,28,17,12,22,10,49,87,45,15,35,17,165,9,26,17,22,38,54,30,43,41,30,7,70,74,47,398,306,0,52,77,119,129,134,178,197,205,244,262,285,325,354,371,384,410,420,469,557,602,618,653,670,841,869,895,914,936,975,1031,1063,11 ...02097+20970,47,67,107,122,147,192,205,218,254,273,297,336,364,387,399,421,432,483,570,616,631,667,701,866,875,914,931,955,993,1047,1077,11 ...aagagggaccaaagttttaccacctggctggtggccatgaacaccaccacaaaggagaagatcattctgcagaccatcaagtggaggatgagagtggacattgaagtggaccccctgcagctgttggg ...248956422143338619801criGriChoV2JP051638.1LT883665v125262842252733229991000unknownunknownsynChinese hamsterCricetulus griseusCricet
chr1166059501166059816musFur1:EZ503442.1-1.1700-16605981616605981601047,42,8,6,31,9,21,19,9,75,0,47,103,118,149,180,189,210,231,240,0278+2780,48,90,98,104,136,148,173,192,203,gggattctctctctgtacccaaacacttccatcccaacctgattttcagccagaagtagggttagaaaccaccaattctagtcatgataaagccacacaaatcagcaaacagagggtcagctgtccaa ...248956422150803701musFur1EZ503442.1GL896927361288036131589961000unknownunknownsynFerretMustela putorius furoMustel

TransMap RNA (transMapRnaV5) Track Description
 

Description

This track contains GenBank mRNA alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. For closer evolutionary distances, the alignments are created using syntenically filtered BLASTZ alignment chains, resulting in a prediction of the orthologous genes in human.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks.

This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here.

Methods

  1. Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available.
  2. For all vertebrate assemblies that had BLASTZ alignment chains and nets to the human (hg38) genome, a subset of the alignment chains were selected as follows:
    • For organisms whose branch distance was no more than 0.5 (as computed by phyloFit, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the netfilter -syn command. The chains corresponding to the selected nets were used for mapping.
    • For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogous regions. The post-alignment filtering step removes some of the duplications.
  3. The pslMap program was used to do a base-level projection of the source transcript alignments via the selected chains to the human genome, resulting in pairwise alignments of the source transcripts to the genome.
  4. The resulting alignments were filtered with pslCDnaFilter with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded.

To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is:

   accession.version-srcUniq.destUniq
Where srcUniq is a number added to make each source alignment unique, and destUniq is added to give the subsequent TransMap alignments unique identifiers.

For example, in the cow genome, there are two alignments of mRNA BC149621.1. These are assigned the identifiers BC149621.1-1 and BC149621.1-2. When these are mapped to the human genome, BC149621.1-1 maps to a single location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic.

Data Access

The raw data for these tracks can be accessed interactively through the Table Browser or the Data Integrator. For automated analysis, the annotations are stored in bigPsl files (containing a number of extra columns) and can be downloaded from our download server, or queried using our API. For more information on accessing track data see our Track Data Access FAQ. The files are associated with these tracks in the following way:

  • TransMap Ensembl - hg38.ensembl.transMapV4.bigPsl
  • TransMap RefGene - hg38.refseq.transMapV4.bigPsl
  • TransMap RNA - hg38.rna.transMapV4.bigPsl
  • TransMap ESTs - hg38.est.transMapV4.bigPsl
Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/transMap/V4/hg38.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout

Credits

This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects.

References

Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246; PMC: PMC2099585

Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656

Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818; PMC: PMC2134963