RetrogeneDB ID: | retro_ggor_2186 | ||
Retrocopy location | Organism: | Gorilla (Gorilla gorilla) | |
| Coordinates: | 5:80424177..80425818(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | YTHDF1 | ||
| Ensembl ID: | ENSGGOG00000008340 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ggor_2186
AGCATGGACACTTAGAGAACAAAAGGACAAGACAGTAAAGTACACAATGATTCTTTGCATCAGAAGGATGTGGTTCATGA
CAATGACTTTCAGCCCTACCTTTCTGGAGAGTCAAATTAGAGTAACAATTACCCTTCAGCGAGTGACCTCTACCTGTCCG
GCTATTACCCACCATCCAGTGGAGTTCCTTAATCCCTCAATGAGGCTCTGTGGTCCACTGCAAGGGACCCTTTGATTCTA
CACCTCATCACCTATGAACAGCTCAGTAACAGAGATCATAATTTTATGCACAATTCTATTTTGGGGTGGCCTTGGGGTCC
AGAGAACAAAATCTATCAGCACAGGTTTAATTTTTACCCCCAAACCCTGTATTCTTGGCAGGGAGGACAAGTGGGTCTCA
AGGGTAGCAGATTCAGAGCTCTACATATGGGAGCAGCTACACCTACCCCCAAGCTCCCTGGGCCACGCAGTCGTTGATGG
GCAGATGGGCTTTCACAGTGACACCCTTAGCAAGGCCCCTGGGGTGAACAGCCTGAAGCAGGGCATGGTCAGCCTGAAAA
TTGGGGATGTCATCTCCTCTGCAGTCAAGACAGTGGGCTCTGTCATCAGCAGTGTGGCACTGATTGGCATCCTTTCTGGC
AATGATGGGACATATGTGAACATGGCAGTTTCAAAGCTGACCTCATGGGCCACCATTGCCAGCAAGCCTGCAAAACCACG
GTCTAAAATGGAAACAAGGAGTGGGCCTGTCATAGGGGGGTGCACTGCCCCCTCCATCTATAAAGCATAACATGGATATT
GACACCCAGGATAACAAGGGGCCTGTGCTGAAGACCCCGGTCCCCCAGGAGACATGATCCTCACAGGCTGTCCTACATCC
CCAGAAGGTGCTTCAGCTTCTCCCAATGAAGCTTCCTGCTTTGGCTCAACCACAGTGTTAGAGCCCTCAGCAGCCACTCC
AGACCTGCTGGATCATTCCTCACGTGGAAATATGGCATTTGGGCAGAGCAGAGGGGCTGACAGTGGTAGTAACTCTCCTG
GAAATACCAAGACTAATTCTGCCCCAAGTGTAAAAAAAGTGAAAGCTGCCCACAGTTATAATCCTAAAGAATTTGACTGG
AATCTTAAAAGTGGACATGTACACATTATAAAGAGCTATTCTGAGGATGACATTCACCACTCCATTAAGTACTCCCTTTT
GTGTAGTACAGAACATGGCACTACTTAGTTGAATAGTCCATTCAGCTCCATAAGCAGCAAGGGGCTGTCTACCTGCCCTT
CGGCATCAGTGGGAGTGAGTATTTCTGTGGGGTGGTGGAGATGAAGTGCTCTGTGGACAGCAGCACCAGTGCCAGAGTCT
GGTCTCAAGACAAATGGAAGGGGAAGTTTGATGTCAAGTGGATTTTTGTCAGTGATGTACCCAATAACCAGCTCAGGCAC
ATCAGACTGGAGAATCATGACAACAAGCCAGTCATAAACCATGAAACACAGGAGGTGCCTTTAGAAAAAGAAAAACAAGT
GCTGAAAATTATTGCTTCCTACAAGCACACAACCTCTATCTTTGATGACTTTTCTCACTACGCGAAATGCCAGGACGAGG
AGGAGGTGATGTGCAAGGAATGACACAATCAAAATAAACAA
ORF - retro_ggor_2186 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.75 % |
| Parental protein coverage: | 99.28 % |
| Number of stop codons detected: | 8 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | SVDTQRTKGQDNKVQNGSLHQKDTVHDNDFEPYLTGQSNQSNSYPSMSDPYLSSYYPPSIGFPYSLNEAP |
| S.DT.RTKGQD.KV.N.SLHQKD.VHDNDF.PYL.G.SN.SN.YPS.SD.YLS.YYPPS.G.P.SLNEA. | |
| Retrocopy | SMDT*RTKGQDSKVHNDSLHQKDVVHDNDFQPYLSGESN*SNNYPSASDLYLSGYYPPSSGVP*SLNEAL |
| Parental | WSTAGDPPIPYLTTYGQLSNGDHHFMHDAVFGQPGGLGNNIYQHRFNFFPE-NPAFSAWGTSGSQGQQTQ |
| WSTA.DP.I..L.TY.QLSN.DH.FMH....G.P.G..N.IYQHRFNF.P..NP.F.A..TSGSQG.Q.Q | |
| Retrocopy | WSTARDPLILHLITYEQLSNRDHNFMHNSILGWPWGPENKIYQHRFNFYPQ<NPVFLAGRTSGSQG*QIQ |
| Parental | SSAYGSSYTYP-PSSLGGTVVDGQPGFHSDTLSKAPGMNSLEQGMVGLKIGDVSSSAVKTVGSVVSSVAL |
| SS.YGSSYTYP.PSSLG..VVDGQ.GFHSDTLSKAPG.NSL.QGMV.LKIGDV.SSAVKTVGS....... | |
| Retrocopy | SSTYGSSYTYP<PSSLGHAVVDGQMGFHSDTLSKAPGVNSLKQGMVSLKIGDVISSAVKTVGSXXXXXXX |
| Parental | TGVLSGNGGTNVNMPVSKPTSWAAIASKPAKPQPKMKTKSGPVMGG-ALPPPPIKHNMDIGTWDNKGPVP |
| ........GT.VNM.VSK.TSWA.IASKPAKP..KM.T.SGPV.GG.ALPPP.IKHNMDI.T.DNKGPV. | |
| Retrocopy | XXXXXXXDGTYVNMAVSKLTSWATIASKPAKPRSKMETRSGPVIGG>ALPPPSIKHNMDIDTQDNKGPVL |
| Parental | KAPVPQQAPSPQAAPQPQQVAQPLPAQPPALAQPQYQSPQQPPQTRWVAPR-NRNAAFGQSGGAGSDSNS |
| K.PVPQ...S.QA...PQ.V.Q.LP...PALAQPQ..SPQQP.QT.W..P....N.AFGQS...G.DS.. | |
| Retrocopy | KTPVPQET*SSQAVLHPQKVLQLLPMKLPALAQPQC*SPQQPLQTCWIIPH<RGNMAFGQS--RGADS-- |
| Parental | PGNVQPNSAPSVESHPVLEKLKAAHSYNPKEFEWNLKSGRVFIIKSYSEDDIHRSIKYSIWCSTEHGNKR |
| .G...P.......S.P...K.KAAHSYNPKEF.WNLKSG.V.IIKSYSEDDIH.SIKYS..CSTEHG... | |
| Retrocopy | -GSNSPGNTKT-NSAPSVKKVKAAHSYNPKEFDWNLKSGHVHIIKSYSEDDIHHSIKYSLLCSTEHGTT* |
| Parental | LDSAFRCMSSKG-PVYLLFSVNGSGHFCGVAEMKSPVDYGTSAGVWSQDKWKGKFDVQWIFVKDVPNNQL |
| L.S.F...SSKG..VYL.F...GS..FCGV.EMK..VD..TSA.VWSQDKWKGKFDV.WIFV.DVPNNQL | |
| Retrocopy | LNSPFSSISSKG<AVYLPFGISGSEYFCGVVEMKCSVDSSTSARVWSQDKWKGKFDVKWIFVSDVPNNQL |
| Parental | RHIRLENNDNKPVTNSRDTQEVPLEKAKQVLKIISSYKHTTSIFDDFAHYEKRQEEEEVVRKERQNRNKQ |
| RHIRLEN.DNKPV.N...TQEVPLEK.KQVLKII.SYKHTTSIFDDF.HY.K.Q.EEEV..KE..N.NKQ | |
| Retrocopy | RHIRLENHDNKPVIN-HETQEVPLEKEKQVLKIIASYKHTTSIFDDFSHYAKCQDEEEVMCKE*HNQNKQ |
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 |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 0 .05 RPM | 50 .11 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 69 .97 RPM |
| SRP007412_heart | 0 .00 RPM | 16 .79 RPM |
| SRP007412_kidney | 0 .08 RPM | 44 .98 RPM |
| SRP007412_liver | 0 .03 RPM | 38 .12 RPM |
| SRP007412_testis | 0 .10 RPM | 49 .94 RPM |
Gorilla gorilla was not studied using ChIP-Seq data.
Gorilla gorilla was not studied using EST data.
Gorilla gorilla was not studied using FANTOM5 data.
retro_ggor_2186 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ggor_2186 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3220 |
| Pan troglodytes | retro_ptro_2170 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000149658 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000008340 | 1 retrocopy |
retro_ggor_2186 ,
|
| Nomascus leucogenys | ENSNLEG00000009975 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000013730 | 1 retrocopy |