RetrogeneDB ID: retro_ecab_260

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:15098661..15100196(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: USP21
• Ensembl ID: ENSECAG00000016189
• Aliases: None
• Description: ubiquitin specific peptidase 21 [Source:HGNC Symbol;Acc:12620]

Sequence

>retro_ecab_260
TTACAACCTCTGCCTCCCCTGTCTGGTCCCCCTGAGGAACGGCTCAAGAAACTGGAGCCAGGACGAGGACCAACCTCAGG
CCCTCGTCCCAGAGGCCCTCTTTGGGCATCTCATGGAGTTCCCCTTCCTGGCTCACTGCCCCCAGCTGTGGCTCTGCCTG
TCCCATCCAGGACGAACCTGGCCCATTCCAGGTCTGTGAGCAGTGGAGACTTGCATCCAATGAGGACTGCCTTGGGAGGG
CACTGTGGCGCTGGAAAGCCAGGGGCTGCGCTGAGCCGCTTGGCACTCTAACCCGAGTCACCCACTTTGAGACGTAGCAC
CTCTCTCCGCCACCTCGGGGCCTTTCCTGGGCCCCCCACCTTGCTCAGCATATGGACAGAGCCCCCTGCTTCCCATGGCT
TCTTCCACGTGATATCTGCCCGGCCCTCTGAGCCTTTCTACTTTGATGACAAGATGGCTCACCACATGCTGCTTCTGGGC
TTTGGTCACATTGGCCTCCCAAATCTGGGAAATACGTGCTTCCTGAATGCTGTGCTGCAGTGTTTGAGCAGCACTGGGTC
TCTTCGGGACTTCTCTCTGTGAAGGGACCTCCGGCAAGAGGTGCCTGGAGGGGGCCGAGCCCAAGAGCTCAATGAAGCCT
TTGCAGATGTGATTGGTGCTCCGTGGCACCCTGACTCCTGCGAAGCTGTGAATGGTGCTGGATGACGAGCTGTCTTCTGG
AAACATGTTCCCTCCTTCTCTGGATATAGCCAGCAGGATGCCCACAAGTTCCTGAAGCTCCTCATGGAGTGGCTGCACCT
TGAAATCAACCAATGAGGCCGCCGGGCTCCGTCAGTCTTGGCCAACAGTCCAGCTCCCTTCTCCACCCCACCAACGGGCT
CTGCTAGAAGAATCTGAGTTAAGTGAAGATGACCGAGCCAACCTAACGTGGAAGTGTTACGTGGAGCAAGAGGACAGCAA
GACTGTGGACCTGTTTGTGGGCCAGTTGAAAAGTTGTCTCTAGTGCCAGGCCTGTGGGTATCGTTCCACGACCTTTGAGG
TTTTTTGTGACCTGTCCCTGTCCATCCCCAAGAACAGATTCACTGGGGGCAAGGTGTCTCTGCAGGATGGTTTCAGCCTT
TTCACCAAGGAAGAACAGCTGGAGTTGGAGAATGCCCCAGTGTGTGACCAATGTCGCAGAAAACATGAAGTACCAAAAAG
TTGACAGTACAAAGATGCCCCCGAATCCTTGTGCTCCGTGTTAATCAATTTTATGCCTCCCGAGGATCCATCAAGAAAAG
TTCAATAGGTGTAGACTTCCCACTGCAGCGACTGAGCCTAGGGGACTTTGCCAGAGATGAAGCCAGAAGCCCCACAGATC
AGAGTATGTCCTTTACAACTACTCCGGCGGGGTCCACTATGGCCACTACACAGCCCTGTGCCGATACCAGACTGGTTGGC
ATGTCTACAATGACTCTCGTGTCTGCCTTGTTAGTGAAGACCAGGTGGCATCCAGTGAAGGCTACATGCTGTTCCAGCTG
ATGCAGGAGCCACCC

Alignment

ORF - retro_ecab_260 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.04 %
• Parental protein coverage: 90.97 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LRPLPPRPGPPEERLKKLELGRGRTSGPRPRGPLRADHGVPLPGSPPPTVALPVPSRTNLTRSKSVSSGD
          L.PLPP..GPPEERLKKLE.GRG.TSGPRPRGPL.A.HGVPLPGS.PP.VALPVPSRTNL..S.SVSSGD
Retrocopy LQPLPPLSGPPEERLKKLEPGRGPTSGPRPRGPLWASHGVPLPGSLPPAVALPVPSRTNLAHSRSVSSGD

Parental  LRPMGIALGGHRGAAELGAALSRLALRPEPPILRRSTSLRRLGGFPGPPTLLSIRTEPPASHGSFHVISG
          L.PM..ALGGH.GA...GAALSRLAL.PE.P.LRRSTSLR.LG.FPGPPTLLSI.TEPPASHG.FHVIS.
Retrocopy LHPMRTALGGHCGAGKPGAALSRLAL*PESPTLRRSTSLRHLGAFPGPPTLLSIWTEPPASHGFFHVISA

Parental  RPSEPFYFDDKMAHHTLLLGSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQEL
          RPSEPFYFDDKMAHH.LLLG.GH.GL.NLGNTCFLNAVLQCLSST..LRDF.L.RD.RQEVPGGGRAQEL
Retrocopy RPSEPFYFDDKMAHHMLLLGFGHIGLPNLGNTCFLNAVLQCLSSTGSLRDFSL*RDLRQEVPGGGRAQEL

Parental  TEAFADVIGALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPIL
          .EAFADVIGA.WHPDSCEAVN....RAVF.K.VPSFSGYSQQDA..FLKLLME.LHLEIN..GRRAP..L
Retrocopy NEAFADVIGAPWHPDSCEAVNGAG*RAVFWKHVPSFSGYSQQDAHKFLKLLMEWLHLEINQ*GRRAPSVL

Parental  ANSPA-PSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRSTTFEVF
          ANSPA.PSPP....ALLEE.ELS.DDRANL.WK.Y.E.EDSK.VDLFVGQLKSCL.CQACGYRSTTFEVF
Retrocopy ANSPA>PSPPHQ-RALLEESELSEDDRANLTWKCYVEQEDSKTVDLFVGQLKSCL*CQACGYRSTTFEVF

Parental  CDLSLPIPKKGFAGGKVSLRDCFSLFTKEEELESENAPVCDRCR-QKTRSTKKLTVQRFPRILVLHLNRF
          CDLSL.IPK..F.GGKVSL.D.FSLFTKEE.LE.ENAPVCD.CR.QKT.STKKLTVQR.PRILVL..N.F
Retrocopy CDLSLSIPKNRFTGGKVSLQDGFSLFTKEEQLELENAPVCDQCR<QKT*STKKLTVQRCPRILVLRVNQF

Parental  SASRGSIKKSSIGVDFPLQRLSLGDFASDKAGDPIYQL-YALCNHSGSVHYGHYTALCRCQTGWHVYNDS
          .ASRGSIKKSSIGVDFPLQRLSLGDFA.D.A..P..Q..Y.L.N.SG.VHYGHYTALCR.QTGWHVYNDS
Retrocopy YASRGSIKKSSIGVDFPLQRLSLGDFARDEARSPTDQS<YVLYNYSGGVHYGHYTALCRYQTGWHVYNDS

Parental  RVSPVSENQVASSEGYVLFYQLMQEPP
          RV..VSE.QVASSEGY.LF.QLMQEPP
Retrocopy RVCLVSEDQVASSEGYMLF-QLMQEPP

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	0.06 RPM	4.31 RPM
SRP021940_cerebellum	0.00 RPM	20.77 RPM
SRP021940_embryo	0.03 RPM	39.33 RPM
SRP021940_placental_villous	0.00 RPM	8.56 RPM
SRP021940_synovial_membrane	0.00 RPM	16.11 RPM
SRP021940_testis	0.51 RPM	35.94 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_260 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_260 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_260 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000016189	1 retrocopy	retro_ecab_260 ,
Nomascus leucogenys	ENSNLEG00000014052	1 retrocopy	retro_nleu_106,