Schema for ucscRetroInfo9
  Database: hg38    Primary Table: ucscRetroInfo9    Row Count: 15,491   Data last updated: 2018-10-19
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 627int(10) unsigned range score of pseudogene with gene col5
strand -char(2) values + or -
thickStart 87548int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 89605int(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 242162106int(11) range parent gene alignment start position col17
gEnd 242164234int(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 5int(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 51int(10) unsigned range repeats in gene col30
coverage 100int(10) unsigned range % of bases that align to gene col31
label 1int(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 0int(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 242088692int(11) range kg alignment start position col45
kEnd 242162417int(11) range kg alignment end position col46
overName nonevarchar(255) values name of overlapping mrna col47
overStart -1int(11) range overlapping mrna start position col48
overExonCover -1int(11) range count of overlapping mrna exons col49
overStrand 0char(2) values strand of overlapping mrna col50
posConf 0float range pvalue for positive col51
polyAlen 22int(10) unsigned range length of polyA col52

Connected Tables and Joining Fields
        hg38.knownGene.name (via ucscRetroInfo9.kgName)
      hg38.ucscRetroAli9.qName (via ucscRetroInfo9.name)
      hg38.ucscRetroCds9.id (via ucscRetroInfo9.name)
      hg38.ucscRetroOrtho9.name (via ucscRetroInfo9.name)
      hg38.ucscRetroSeq9.acc (via ucscRetroInfo9.name)
      hg38.refGene.name (via ucscRetroInfo9.refSeq)

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEnditemRgbblockCountblockSizeschromStartsretroExonCountaxtScoretypegChromgStartgEndgStrandparentSpliceCountgeneOverlappolyApolyAstartexonCoverintronCountbestAliCountmatchesqSizeqEndtRepscoveragelabelmilliBadalignGapCountprocessedIntronsconservedSpliceSitesmaxOverlaprefSeqrStartrEndmgcmStartmEndkgNamekStartkEndoverNameoverStartoverExonCoveroverStrandposConfpolyAlen
chr18754889605AK021903.1-1627-87548896050,0,012057,0,1192933expressed weak noOrfchr2242162106242164234+201922052032205720575110019880100noRefSeq-1-1noMgc-1-1noKg242088692242162417none-1-10022
chr1131067134836NM_015125.3-11350+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 ...5190732expressed weak noOrfchr194228466442295797+460211140225885473547145518392412064NM_0151254228466442295797ENST00000575354.24228466442295797ENST00000575354.64228466442295797none-1-10027
chr1135466135765AK128836.1-3632-1354661357650,0,0333,136,129,0,33,170,120194expressed strong noOrfchr76375797863767286+402-663022664028310607-2816020299noRefSeq-1-1noMgc-1-1noKg-1-1NR_0399831347723-02
chr1158251158676BC038571.1-3655-1582511586760,0,011119,13,12,19,10,17,12,16,17,142,44,0,119,135,147,166,176,193,206,222,239,381,126758expressed weak noOrfchr73973363439781300+10046740134011541006283617720210NR_0269993973356739794623ENST00000340510.43973363139793092ENST00000340510.83973356739794623none-1-1004
chr1258511259036AK130965.1-1938-2585402589030,0,0623,47,48,290,86,29,0,23,70,118,410,496,142781expressed weakchr172871999228723935+8011-150248053853879719050400NM_0009842871998128724356ENST00000582718.12872148628722877ENST00000394938.82872029028724356none-1-101313
chr1265765266415AK021903.1-3542-2657212658080,0,02198,452,0,198,158050expressed weakchr2242162106242164234+203-3205626205716142831193101053noRefSeq-1-1noMgc-1-1noKg242088692242162417none-1-1033
chr1347908348441AK130965.1-2918-3481873484510,0,0576,188,152,86,29,0,76,264,418,504,138945expressed weakchr172871999228723935+806-7450243553853809818120400NM_0009842871998128724356ENST00000582718.12872148628722877ENST00000394938.82872029028724356none-1-1077
chr1355147355797AK021903.1-4525-3551033551900,0,02198,452,0,198,158469expressed weakchr2242162106242164234+203-320562820571614423119340100noRefSeq-1-1noMgc-1-1noKg242088692242162417none-1-1033
chr1367880368170AK126884.1-8522+3678803681700,0,0852,21,18,10,29,42,33,68,0,53,76,94,110,139,188,222,110737expressed weak noOrfchr124987509149880314-6012-6420119334484510717070200noRefSeq-1-1noMgc-1-1noKg-1-1none-1-10017
chr1439768440208AK308843.1-1581+4397684402080,0,0540,54,128,124,87,0,44,98,229,353,132179pseudogenechr10102743957102832094+12032301378136044803118570200NM_017787102776130102816264ENST00000369889.4102776248102816264ENST00000369889.5102776130102816264none-1-1003

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