RetrogeneDB ID: retro_ecab_314

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:49751152..49752749(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000018291
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UPF1
• Ensembl ID: ENSECAG00000010639
• Aliases: None
• Description: UPF1 regulator of nonsense transcripts homolog (yeast) [Source:HGNC Symbol;Acc:9962]

Sequence

>retro_ecab_314
ATTGAGAAGATCAGCACCAAAAGCCGCAAGACCATCGACTCCCTGGTGTCCTTCCTGGCCCTGCAGAAACGGATCAGGAA
CATTGATAGATGGCATGCCAGAAGCTGCTGCTGCAGCTGAAGGATGAGACTAGGGAGCTGTCATCTGCAGACAAGAAGCA
GTACCCGGCCCTAAAGCACACTGCCAAGAGAGAGCAGCTCATCAAAGCAGATGTCATCTGCTGCACGTGGCTGGGTGCAG
ATGACCCAAGGTTCGCCAAGATGCAGTTCTGCTCCATTTTAATTGAGAGAAGTACTCAGGCTGCCGAGCCAGAGTGCGTG
GTCCCTGTGGTCCTCAGAGCCAAGCAGCTGATCCTCGTGGGCAACCACTGCCAGCTAGGCCTCATGGTGATGCGCAAAAA
GGCTGCCAGGGCTGCGCTGTCCCAGTCACTCTTTGAGCACCTGGTGGTGTTGGGCATCCATGCCATCCGCCTCATCTGCC
TCTAGGTCCAGTATCGGATGCACGCTATGCTAAGCACCTTCCCACCCATCATCTTCTATGAGGGCTCCCTTCAGAACAGC
ATCACTGCAGCAGATTGTGTGAAGGGGTCTGACTTTCAGTAGCCCCAACCTGATAAACTGATGATCTACGTGACCCAGGG
TGAGGAGGAGATGGCCAGCTTGGGGACCTCCTACCTGAACAGGATGGAAGCTGCCAACATGGAGATCGCCATGAAGTTAC
TGAAAGCAGGTGCCAAGCCAGACCAGATTGACATCATCATGCCCTATGAGGGTTGGCGCTCCTACCTGGTGCAGTACATG
CACTTCATTGGCTCCCTGTACACCAAGCTCTACCAGGAGGTGGAGATCGCCAGCATGGACACGTTCCAGGAGCATGAGAA
GGACTTTGTCATCCTCTCCTGCATGTGGGCAAATGAGCACCAAGGCATTGGGTTTTTAAACAACCCCAGGCAGTTTAATG
TGGCCCTGACCAGAGCACAATATGGAGTCATTATTGTGGGCAACCCAAAGGCCCTGCCCAGGAACCACCTGCTGAACTAC
TACAAGGAGCAGAAGGTGCTGGTGAAGGAACCCCTGAATAGCCTGTGGGAGAGCCCCATGCAGTTCAGCAAGCCCAGGGT
GCTGGTCAACACCATCAATCTGGGAGCCCTCTTCATGACAACAGCCACGTATGACCCCAGGAGGCCATTATCCCAGGATC
TGTCTATGATCAGAGCATCCAGGGCTGGCCCTTGAACACTACTTCCAGACCCACAATCAGTGGGCACGATGAGTGCTGGG
CCCAGCCATGTGGCCGCCGTGAGCACTCCCCATCCCCTTCAACCTGCTCATGTCACCCATGCCACCACTGGGATATTTTG
GACAAGCTAACAGGGCCAGCAACAGGCCAGGACACCCCAAAAGGCAAAACTGGTTGTGGGAGATGCCAGAAGAACAACTT
TGAGCATCCTGGGCCCAGCCAGAGGAATCTCTCCAACAGCCAGTTCAGCCAGGACTTGGTGTCACAGCTGTTTTCACAGG
GCCCCCTGATGCCAGGCTACATCTCCATGAACTAGCCCTGCTGGATGAGCTAGCCCGGCCTCTCCCAGCCCAAGGTA

Alignment

ORF - retro_ecab_314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.61 %
• Parental protein coverage: 51.54 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VVRLCAKSREAIDSPVSFLALHNQIRNMDS-MPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMN
          ......KSR..IDS.VSFLAL...IRN.D..M.....L.QLKDET.ELSSAD.K.Y.ALK.TA.RE.L..
Retrocopy IEKISTKSRKTIDSLVSFLALQKRIRNIDR<MACQKLLLQLKDETRELSSADKKQYPALKHTAKREQLIK

Parental  ADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAG
          ADVICCT..GA.DPR.AKMQF.SILI..STQA.EPEC.VPVVL.AKQLILVG.HCQLG..VM.KKAA.A.
Retrocopy ADVICCTWLGADDPRFAKMQFCSILIERSTQAAEPECVVPVVLRAKQLILVGNHCQLGLMVMRKKAARAA

Parental  LSQSLFERLVVLGIRPIRLQ---VQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPM
          LSQSLFE.LVVLGI..IRL....VQYRMH..LS.FP..IFYEGSLQN..TAAD.V.KG.DFQ.PQPDK..
Retrocopy LSQSLFEHLVVLGIHAIRLICL*VQYRMHAMLSTFPPIIFYEGSLQNSITAADCV-KGSDFQ*PQPDK-L

Parental  FFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTK
          ..YVTQG.EE.AS.GTSYLNR.EAAN.E.I..KLLKAGAKPDQI.II.PYEG.RSYLVQYM.F.GSL.TK
Retrocopy MIYVTQGEEEMASLGTSYLNRMEAANME-IAMKLLKAGAKPDQIDIIMPYEGWRSYLVQYMHFIGSLYTK

Parental  LYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWN
          LYQEVEIAS.D.FQ..EKDF.ILSC..ANEHQGIGFLN.PR..NVALTRA.YGVIIVGNPKAL......N
Retrocopy LYQEVEIASMDTFQEHEKDFVILSCMWANEHQGIGFLNNPRQFNVALTRAQYGVIIVGNPKALPR----N

Parental  HLLNYYKEQKVLVEGPLNNLRESLMQFSKPRKLVNTINPGARFMTTAMYDAR-EAIIPGSVYDRSSQGRP
          HLLNYYKEQKVLV..PLN.L.ES.MQFSKPR.LVNTIN.GA.FMTTA.YD.R.EAIIPGSVYD.S.QG.P
Retrocopy HLLNYYKEQKVLVKEPLNSLWESPMQFSKPRVLVNTINLGALFMTTATYDPR<EAIIPGSVYDQSIQGWP

Parental  SNM-YFQTHDQ-IGMISAGPSHVAAMN-IPIPFNLVMPPMPPPGYFGQAN-GPAAGRGTPKGKTGRGGRQ
          .N..YFQTH.Q..G..SAGPSHVAA....PIPFNL.M.PMPP.GYFGQAN.GPA.G..TPKGKTG.G..Q
Retrocopy LNT<YFQTHNQ<VGTMSAGPSHVAAVS>LPIPFNLLMSPMPPLGYFGQAN>GPATGQDTPKGKTGCGRCQ

Parental  KNRFGLPGPSQTTLPNSQASQDVASQPFSQGALTQGYISMSQPSQMSQPGLSQPEL
          KN.F..PGPSQ..L.NSQ.SQD..SQ.FSQG.L..GYISM..P..MS.PGLSQP..
Retrocopy KNNFEHPGPSQRNLSNSQFSQDLVSQLFSQGPLMPGYISMN*PCWMS*PGLSQPKV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.00 RPM	80.52 RPM
SRP021940_cerebellum	0.00 RPM	177.66 RPM
SRP021940_embryo	0.03 RPM	170.77 RPM
SRP021940_placental_villous	0.00 RPM	68.37 RPM
SRP021940_synovial_membrane	0.05 RPM	147.72 RPM
SRP021940_testis	0.06 RPM	414.54 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_314 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_314 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_314 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010639	1 retrocopy	retro_ecab_314 ,