Schema for ucscRetroInfo5
  Database: hg19    Primary Table: ucscRetroInfo5    Row Count: 13,742   Data last updated: 2013-04-18
Format description: Retrogenes based on cDNA alignments that are expressed or processed pseudogenes.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
chrom chr1varchar(255) values Reference sequence chromosome or scaffold col1
chromStart 87548int(10) unsigned range pseudogene alignment start position col2
chromEnd 89605int(10) unsigned range pseudogene alignment end position col3
name AK021903.1-1varchar(255) values Name of pseudogene col4
score 625int(10) unsigned range score of pseudogene with gene col5
strand -char(2) values + or -
thickStart 88161int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 88866int(10) unsigned range End of where display should be thick (stop codon)
reserved 0int(10) unsigned range Always zero for now
blockCount 1int(11) range Number of blocks
blockSizes 2057,longblob   Comma separated list of block sizes
chromStarts 0,longblob   Start positions relative to chromStart
retroExonCount 1int(11) range number of exons in retroGene col13
axtScore 192933int(11) range blastz score, parent mrna aligned to pseudogene col14
type expressed weak noOrfvarchar(255) values type of evidence col15
gChrom chr2varchar(255) values chromosome name for parent gene col16
gStart 243171771int(11) range parent gene alignment start position col17
gEnd 243173899int(11) range parent gene alignment end position col18
gStrand -char(2) values strand of parent gene col19
parentSpliceCount 2int(10) unsigned range # of splice sites in parent gene col20
geneOverlap 0int(10) unsigned range bases overlapping col21
polyA 19int(10) unsigned range count of As in polyA col22
polyAstart 2int(11) range start of polyA, relative to end of pseudogene col23
exonCover 2int(11) range number of exons in parent gene covered col24
intronCount 0int(10) unsigned range number of introns in pseudogene col25
bestAliCount 3int(10) unsigned range number of good mrnas aligning col26
matches 2032int(10) unsigned range matches + repMatches col27
qSize 2057int(10) unsigned range aligning bases in pseudogene col28
qEnd 2057int(10) unsigned range end of cdna alignment col29
tReps 50int(10) unsigned range repeats in gene col30
coverage 100int(10) unsigned range % of bases that align to gene col31
label -2int(11) range 1=pseudogene,-1 not pseudogene -2 expressed retroGene col32
milliBad 988int(10) unsigned range milliBad score, pseudogene aligned to genome col33
alignGapCount 0int(11) range simple intron count col34
processedIntrons 1int(11) range count of introns removed via retrotransposition col35
conservedSpliceSites 0int(11) range conserved splice site count col36
maxOverlap 311int(11) range largest overlap with another mrna col37
refSeq noRefSeqvarchar(255) values Name of closest regSeq to gene col38
rStart -1int(11) range refSeq alignment start position col39
rEnd -1int(11) range refSeq alignment end position col40
mgc noMgcvarchar(255) values Name of closest mgc to gene col41
mStart -1int(11) range mgc alignment start position col42
mEnd -1int(11) range mgc alignment end position col43
kgName noKgvarchar(255) values Name of closest knownGene to gene col44
kStart -1int(11) range kg alignment start position col45
kEnd -1int(11) range kg alignment end position col46
overName AK125248varchar(255) values name of overlapping mrna col47
overStart 89294int(11) range overlapping mrna start position col48
overExonCover 11int(11) range count of overlapping mrna exons col49
overStrand -char(2) values strand of overlapping mrna col50
posConf 22float range pvalue for positive col51
polyAlen 22int(10) unsigned range length of polyA col52

Connected Tables and Joining Fields
        hg19.ucscRetroAli5.qName (via ucscRetroInfo5.name)
      hg19.ucscRetroCds5.id (via ucscRetroInfo5.name)
      hg19.ucscRetroExpressed5.name (via ucscRetroInfo5.name)
      hg19.ucscRetroOrtho5.name (via ucscRetroInfo5.name)
      hg19.ucscRetroSeq5.acc (via ucscRetroInfo5.name)
      hg19.refGene.name (via ucscRetroInfo5.refSeq)

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEnditemRgbblockCountblockSizeschromStartsretroExonCountaxtScoretypegChromgStartgEndgStrandparentSpliceCountgeneOverlappolyApolyAstartexonCoverintronCountbestAliCountmatchesqSizeqEndtRepscoveragelabelmilliBadalignGapCountprocessedIntronsconservedSpliceSitesmaxOverlaprefSeqrStartrEndmgcmStartmEndkgNamekStartkEndoverNameoverStartoverExonCoveroverStrandposConfpolyAlen
chr18754889605AK021903.1-1625-88161888660,0,012057,0,1192933expressed weak noOrfchr2243171771243173899-2019220320322057205750100-2988010311noRefSeq-1-1noMgc-1-1noKg-1-1AK1252488929411-2222
chr1131067134836NM_015125.3-11354+1310671348360,0,04732,28,87,12,246,220,35,95,33,67,112,59,176,7,93,79,92,61,27,112,149,233,21,47,56,7,9,7,7,8,12,11,28,12,6,36,66,53,45,52,22,11,9, ...0,32,60,147,159,405,626,666,761,794,862,974,1033,1209,1216,1309,1388,1480,1541,1571,1683,1898,2131,2152,2199,2262,2283,2366,2399 ...5190727expressed weak noOrfchr194278881642799949+460211140125885473547115518392412064NM_0151254278881642799949ENST000001607404278817142799948uc002otf.14278881642799949none-1-10027
chr1228262228787AK130965.1-1948-2282912286540,0,0623,47,48,290,86,29,0,23,70,118,410,496,142781expressed weakchr172704701027050953+8011-150148053853809719050400NM_0009842704699927051374ENST000004738962704772427050652uc021ttu.12704730827051374none-1-101313
chr1235516236166AK021903.1-3559-2354722355590,0,02198,452,0,198,158050expressed weakchr2243171771243173899-203-3203626205716141631193101053noRefSeq-1-1noMgc-1-1noKg-1-1none-1-1033
chr1321020321264AK302511.1-14656+3212033212780,0,0211,233,0,11,122680expressed weakchr1663825679708-1205104204240206697201119100200NR_028327661138665731ENST00000416385677192685396uc002khh.3661138679736none-1-1077
chr1321438322024BC018677.1-4759-3216893217760,0,01620,40,7,14,32,6,104,33,17,85,35,8,60,23,53,13,0,35,75,82,97,129,140,244,278,296,381,421,431,491,514,573,125946expressed weakchr24738730747403650-1005-15401419116172424717620300NM_0017434738722047403740ENST000004602184738730247401346uc002rvt.24738722047403740none-1-1066
chr1326584328412BC054485.1-30632+3265843284120,0,01336,31,23,20,30,11,13,7,27,4,12,169,1385,0,36,78,105,125,155,182,201,228,258,262,274,443,1152514expressed shufflechr169023575190238406+404110201167021382073082-29400101731noRefSeq-1-1noMgc-1-1uc021tmw.19023709190238407NR_0283273238914+05
chr1328517332282NM_015125.3-21356-3285173322820,0,046404,17,40,18,8,34,52,45,53,66,36,6,12,28,11,12,8,7,7,9,7,56,47,21,233,149,112,27,61,92,79,93,7,176,59,112,67,33,95,35,220,246,12 ...0,404,421,701,764,801,848,900,945,998,1064,1126,1135,1202,1269,1312,1331,1359,1392,1473,1496,1510,1566,1613,1634,1933,2082,2197, ...5192437expressed weak noOrfchr194278881642799949+46024-4140125955473547115518422412064NM_0151254278881642799949ENST000001607404278817142799948uc002otf.14278881642799949none-1-10033
chr1379128379568AK308843.1-1586-3791283795680,0,0587,124,128,54,40,0,87,214,342,400,132179pseudogenechr10104503714104591851+806-65301378136044803118570200NM_017787104535887104576021ENST00000369889104536005104576021uc001kwe.4104535887104576021none-1-1009
chr1470895471368AK312123.1-2869+4708854711490,0,0529,86,152,188,16,0,29,117,269,457,137720expressed weakchr172704701027050660+600140243548447809719160300NM_0009842704699927051374ENST000004738962704772427050652uc021ttu.12704730827051374none-1-1022

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.