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 summary: | ||
| Parental gene symbol: | USP21 | ||
| Ensembl ID: | ENSECAG00000016189 | ||
| Aliases: | None | ||
| Description: | ubiquitin specific peptidase 21 [Source:HGNC Symbol;Acc:12620] |
Retrocopy-Parental alignment summary:
>retro_ecab_260
TTACAACCTCTGCCTCCCCTGTCTGGTCCCCCTGAGGAACGGCTCAAGAAACTGGAGCCAGGACGAGGACCAACCTCAGG
CCCTCGTCCCAGAGGCCCTCTTTGGGCATCTCATGGAGTTCCCCTTCCTGGCTCACTGCCCCCAGCTGTGGCTCTGCCTG
TCCCATCCAGGACGAACCTGGCCCATTCCAGGTCTGTGAGCAGTGGAGACTTGCATCCAATGAGGACTGCCTTGGGAGGG
CACTGTGGCGCTGGAAAGCCAGGGGCTGCGCTGAGCCGCTTGGCACTCTAACCCGAGTCACCCACTTTGAGACGTAGCAC
CTCTCTCCGCCACCTCGGGGCCTTTCCTGGGCCCCCCACCTTGCTCAGCATATGGACAGAGCCCCCTGCTTCCCATGGCT
TCTTCCACGTGATATCTGCCCGGCCCTCTGAGCCTTTCTACTTTGATGACAAGATGGCTCACCACATGCTGCTTCTGGGC
TTTGGTCACATTGGCCTCCCAAATCTGGGAAATACGTGCTTCCTGAATGCTGTGCTGCAGTGTTTGAGCAGCACTGGGTC
TCTTCGGGACTTCTCTCTGTGAAGGGACCTCCGGCAAGAGGTGCCTGGAGGGGGCCGAGCCCAAGAGCTCAATGAAGCCT
TTGCAGATGTGATTGGTGCTCCGTGGCACCCTGACTCCTGCGAAGCTGTGAATGGTGCTGGATGACGAGCTGTCTTCTGG
AAACATGTTCCCTCCTTCTCTGGATATAGCCAGCAGGATGCCCACAAGTTCCTGAAGCTCCTCATGGAGTGGCTGCACCT
TGAAATCAACCAATGAGGCCGCCGGGCTCCGTCAGTCTTGGCCAACAGTCCAGCTCCCTTCTCCACCCCACCAACGGGCT
CTGCTAGAAGAATCTGAGTTAAGTGAAGATGACCGAGCCAACCTAACGTGGAAGTGTTACGTGGAGCAAGAGGACAGCAA
GACTGTGGACCTGTTTGTGGGCCAGTTGAAAAGTTGTCTCTAGTGCCAGGCCTGTGGGTATCGTTCCACGACCTTTGAGG
TTTTTTGTGACCTGTCCCTGTCCATCCCCAAGAACAGATTCACTGGGGGCAAGGTGTCTCTGCAGGATGGTTTCAGCCTT
TTCACCAAGGAAGAACAGCTGGAGTTGGAGAATGCCCCAGTGTGTGACCAATGTCGCAGAAAACATGAAGTACCAAAAAG
TTGACAGTACAAAGATGCCCCCGAATCCTTGTGCTCCGTGTTAATCAATTTTATGCCTCCCGAGGATCCATCAAGAAAAG
TTCAATAGGTGTAGACTTCCCACTGCAGCGACTGAGCCTAGGGGACTTTGCCAGAGATGAAGCCAGAAGCCCCACAGATC
AGAGTATGTCCTTTACAACTACTCCGGCGGGGTCCACTATGGCCACTACACAGCCCTGTGCCGATACCAGACTGGTTGGC
ATGTCTACAATGACTCTCGTGTCTGCCTTGTTAGTGAAGACCAGGTGGCATCCAGTGAAGGCTACATGCTGTTCCAGCTG
ATGCAGGAGCCACCC
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 |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
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 |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_260 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_260 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_260 has 0 orthologous retrocopies within eutheria group .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 |