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 symbol: YTHDF1
• Ensembl ID: ENSGGOG00000008340
• Aliases: None
• Description: None

Sequence

>retro_ggor_2186
AGCATGGACACTTAGAGAACAAAAGGACAAGACAGTAAAGTACACAATGATTCTTTGCATCAGAAGGATGTGGTTCATGA
CAATGACTTTCAGCCCTACCTTTCTGGAGAGTCAAATTAGAGTAACAATTACCCTTCAGCGAGTGACCTCTACCTGTCCG
GCTATTACCCACCATCCAGTGGAGTTCCTTAATCCCTCAATGAGGCTCTGTGGTCCACTGCAAGGGACCCTTTGATTCTA
CACCTCATCACCTATGAACAGCTCAGTAACAGAGATCATAATTTTATGCACAATTCTATTTTGGGGTGGCCTTGGGGTCC
AGAGAACAAAATCTATCAGCACAGGTTTAATTTTTACCCCCAAACCCTGTATTCTTGGCAGGGAGGACAAGTGGGTCTCA
AGGGTAGCAGATTCAGAGCTCTACATATGGGAGCAGCTACACCTACCCCCAAGCTCCCTGGGCCACGCAGTCGTTGATGG
GCAGATGGGCTTTCACAGTGACACCCTTAGCAAGGCCCCTGGGGTGAACAGCCTGAAGCAGGGCATGGTCAGCCTGAAAA
TTGGGGATGTCATCTCCTCTGCAGTCAAGACAGTGGGCTCTGTCATCAGCAGTGTGGCACTGATTGGCATCCTTTCTGGC
AATGATGGGACATATGTGAACATGGCAGTTTCAAAGCTGACCTCATGGGCCACCATTGCCAGCAAGCCTGCAAAACCACG
GTCTAAAATGGAAACAAGGAGTGGGCCTGTCATAGGGGGGTGCACTGCCCCCTCCATCTATAAAGCATAACATGGATATT
GACACCCAGGATAACAAGGGGCCTGTGCTGAAGACCCCGGTCCCCCAGGAGACATGATCCTCACAGGCTGTCCTACATCC
CCAGAAGGTGCTTCAGCTTCTCCCAATGAAGCTTCCTGCTTTGGCTCAACCACAGTGTTAGAGCCCTCAGCAGCCACTCC
AGACCTGCTGGATCATTCCTCACGTGGAAATATGGCATTTGGGCAGAGCAGAGGGGCTGACAGTGGTAGTAACTCTCCTG
GAAATACCAAGACTAATTCTGCCCCAAGTGTAAAAAAAGTGAAAGCTGCCCACAGTTATAATCCTAAAGAATTTGACTGG
AATCTTAAAAGTGGACATGTACACATTATAAAGAGCTATTCTGAGGATGACATTCACCACTCCATTAAGTACTCCCTTTT
GTGTAGTACAGAACATGGCACTACTTAGTTGAATAGTCCATTCAGCTCCATAAGCAGCAAGGGGCTGTCTACCTGCCCTT
CGGCATCAGTGGGAGTGAGTATTTCTGTGGGGTGGTGGAGATGAAGTGCTCTGTGGACAGCAGCACCAGTGCCAGAGTCT
GGTCTCAAGACAAATGGAAGGGGAAGTTTGATGTCAAGTGGATTTTTGTCAGTGATGTACCCAATAACCAGCTCAGGCAC
ATCAGACTGGAGAATCATGACAACAAGCCAGTCATAAACCATGAAACACAGGAGGTGCCTTTAGAAAAAGAAAAACAAGT
GCTGAAAATTATTGCTTCCTACAAGCACACAACCTCTATCTTTGATGACTTTTCTCACTACGCGAAATGCCAGGACGAGG
AGGAGGTGATGTGCAAGGAATGACACAATCAAAATAAACAA

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2186 was not experimentally validated.

Homology

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

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000149658	1 retrocopy	retro_hsap_3220,
Gorilla gorilla	ENSGGOG00000008340	1 retrocopy	retro_ggor_2186 ,
Nomascus leucogenys	ENSNLEG00000009975	1 retrocopy	retro_nleu_2724,
Pan troglodytes	ENSPTRG00000013730	1 retrocopy	retro_ptro_2170,