RetrogeneDB ID:
retro_ecab_314
Organism:
Horse ( Equus_caballus )
Location:
14:49751152-49752749 (-)
Status:
KNOWN_PSEUDOGENE
Aliases:
No gene alias available
Located in intron of:
None
Alignment summary

Identity:
71.61 %
Coverage:
51.54 %
Frameshifts:
6
Stop codons:
4


Parental gene:
Parental gene symbol:
UPF1
Parental gene aliases:
No gene alias available
Parental gene description:
UPF1 regulator of nonsense transcripts homolog (yeast) [Source:HGNC Symbol;Acc:9962]

Genomic region (view in browser)





>retro_ecab_314
ATTGAGAAGATCAGCACCAAAAGCCGCAAGACCATCGACTCCCTGGTGTCCTTCCTGGCC
CTGCAGAAACGGATCAGGAACATTGATAGATGGCATGCCAGAAGCTGCTGCTGCAGCTGA
AGGATGAGACTAGGGAGCTGTCATCTGCAGACAAGAAGCAGTACCCGGCCCTAAAGCACA
CTGCCAAGAGAGAGCAGCTCATCAAAGCAGATGTCATCTGCTGCACGTGGCTGGGTGCAG
ATGACCCAAGGTTCGCCAAGATGCAGTTCTGCTCCATTTTAATTGAGAGAAGTACTCAGG
CTGCCGAGCCAGAGTGCGTGGTCCCTGTGGTCCTCAGAGCCAAGCAGCTGATCCTCGTGG
GCAACCACTGCCAGCTAGGCCTCATGGTGATGCGCAAAAAGGCTGCCAGGGCTGCGCTGT
CCCAGTCACTCTTTGAGCACCTGGTGGTGTTGGGCATCCATGCCATCCGCCTCATCTGCC
TCTAGGTCCAGTATCGGATGCACGCTATGCTAAGCACCTTCCCACCCATCATCTTCTATG
AGGGCTCCCTTCAGAACAGCATCACTGCAGCAGATTGTGTGAAGGGGTCTGACTTTCAGT
AGCCCCAACCTGATAAACTGATGATCTACGTGACCCAGGGTGAGGAGGAGATGGCCAGCT
TGGGGACCTCCTACCTGAACAGGATGGAAGCTGCCAACATGGAGATCGCCATGAAGTTAC
TGAAAGCAGGTGCCAAGCCAGACCAGATTGACATCATCATGCCCTATGAGGGTTGGCGCT
CCTACCTGGTGCAGTACATGCACTTCATTGGCTCCCTGTACACCAAGCTCTACCAGGAGG
TGGAGATCGCCAGCATGGACACGTTCCAGGAGCATGAGAAGGACTTTGTCATCCTCTCCT
GCATGTGGGCAAATGAGCACCAAGGCATTGGGTTTTTAAACAACCCCAGGCAGTTTAATG
TGGCCCTGACCAGAGCACAATATGGAGTCATTATTGTGGGCAACCCAAAGGCCCTGCCCA
GGAACCACCTGCTGAACTACTACAAGGAGCAGAAGGTGCTGGTGAAGGAACCCCTGAATA
GCCTGTGGGAGAGCCCCATGCAGTTCAGCAAGCCCAGGGTGCTGGTCAACACCATCAATC
TGGGAGCCCTCTTCATGACAACAGCCACGTATGACCCCAGGAGGCCATTATCCCAGGATC
TGTCTATGATCAGAGCATCCAGGGCTGGCCCTTGAACACTACTTCCAGACCCACAATCAG
TGGGCACGATGAGTGCTGGGCCCAGCCATGTGGCCGCCGTGAGCACTCCCCATCCCCTTC
AACCTGCTCATGTCACCCATGCCACCACTGGGATATTTTGGACAAGCTAACAGGGCCAGC
AACAGGCCAGGACACCCCAAAAGGCAAAACTGGTTGTGGGAGATGCCAGAAGAACAACTT
TGAGCATCCTGGGCCCAGCCAGAGGAATCTCTCCAACAGCCAGTTCAGCCAGGACTTGGT
GTCACAGCTGTTTTCACAGGGCCCCCTGATGCCAGGCTACATCTCCATGAACTAGCCCTG
CTGGATGAGCTAGCCCGGCCTCTCCCAGCCCAAGGTA

Library Expression (reads per million mapped reads)
SRP021940_articular_cartilage 0.0
SRP021940_cerebellum 0.0
SRP021940_embryo 0.02
SRP021940_placental_villous 0.0
SRP021940_synovial_membrane 0.05
SRP021940_testis 0.06

Parental protein coverage





Changes in the retrocopy sequence






Parental protein
VVRLCAKSREAIDSPVSFLALHNQIRNMDS-MPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDEST
......KSR..IDS.VSFLAL...IRN.D..M.....L.QLKDET.ELSSAD.K.Y.ALK.TA.RE.L..ADVICCT..GA.DPR.AKMQF.SILI..ST
Retrocopy
IEKISTKSRKTIDSLVSFLALQKRIRNIDR/MACQKLLLQLKDETRELSSADKKQYPALKHTAKREQLIKADVICCTWLGADDPRFAKMQFCSILIERST


Parental protein
QATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQ---VQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFD
QA.EPEC.VPVVL.AKQLILVG.HCQLG..VM.KKAA.A.LSQSLFE.LVVLGI..IRL....VQYRMH..LS.FP..IFYEGSLQN..TAAD.V.KG.D
Retrocopy
QAAEPECVVPVVLRAKQLILVGNHCQLGLMVMRKKAARAALSQSLFEHLVVLGIHAIRLICL*VQYRMHAMLSTFPPIIFYEGSLQNSITAADCV-KGSD


Parental protein
FQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDF
FQ.PQPDK....YVTQG.EE.AS.GTSYLNR.EAAN.E.I..KLLKAGAKPDQI.II.PYEG.RSYLVQYM.F.GSL.TKLYQEVEIAS.D.FQ..EKDF
Retrocopy
FQ*PQPDK-LMIYVTQGEEEMASLGTSYLNRMEAANME-IAMKLLKAGAKPDQIDIIMPYEGWRSYLVQYMHFIGSLYTKLYQEVEIASMDTFQEHEKDF


Parental protein
IILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLMQFSKPRKLVNTINPGARFMTTAMYD
.ILSC..ANEHQGIGFLN.PR..NVALTRA.YGVIIVGNPKAL......NHLLNYYKEQKVLV..PLN.L.ES.MQFSKPR.LVNTIN.GA.FMTTA.YD
Retrocopy
VILSCMWANEHQGIGFLNNPRQFNVALTRAQYGVIIVGNPKALPR----NHLLNYYKEQKVLVKEPLNSLWESPMQFSKPRVLVNTINLGALFMTTATYD


Parental protein
AR-EAIIPGSVYDRSSQGRPSNM-YFQTHDQ-IGMISAGPSHVAAMN-IPIPFNLVMPPMPPPGYFGQAN-GPAAGRGTPKGKTGRGGRQKNRFGLPGPS
.R.EAIIPGSVYD.S.QG.P.N..YFQTH.Q..G..SAGPSHVAA....PIPFNL.M.PMPP.GYFGQAN.GPA.G..TPKGKTG.G..QKN.F..PGPS
Retrocopy
PR/EAIIPGSVYDQSIQGWPLNT/YFQTHNQ/VGTMSAGPSHVAAVS\LPIPFNLLMSPMPPLGYFGQAN\GPATGQDTPKGKTGCGRCQKNNFEHPGPS


Parental protein
QTTLPNSQASQDVASQPFSQGALTQGYISMSQPSQMSQPGLSQPEL
Q..L.NSQ.SQD..SQ.FSQG.L..GYISM..P..MS.PGLSQP..
Retrocopy
QRNLSNSQFSQDLVSQLFSQGPLMPGYISMN*PCWMS*PGLSQPKV


Legend:
*
Stop codon
\
Forward frameshift by one nucleotide
/
Reverse frameshift by one nucleotide