RetrogeneDB ID: retro_ptro_2170

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:97630219..97631861(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YTHDF1
• Ensembl ID: ENSPTRG00000013730
• Aliases: None
• Description: None

Sequence

>retro_ptro_2170
AGCATGGACACTTAGAGAACAAAAGGACGAGACAGTAAAGTACACAATGATTCTTTGCATCAGAAGGATGTGGTTCATGA
CAATGACTTTCAGCCCTACCTTTCTGGAGAGTCAAATTAGAGTAACAATTACCCTTCAGCGAGTGACCTCTGCCTGTCCG
GCTATTACCCACCATCCACTGGAGTTCCTTAATCCCTCAATGAGGCTCTGTGGTCCACTGCAAGGGACCCTTTGATTCTA
CACCTCATCACCTATGAACAGCTCAGTAACAGAGATCATAATTTTATGCACAATTCTATTTTGGGGTGGCCTTGGGGTCC
AGAGAACAAAATCTATCAGCACAGGTTTAATTTTTACCCCCAAACCCTGTATTCTTGGCATGGAGGACAAGTGGGTCTCA
AGGGTAGCAGATTCAGAGCTCTACATATGGGAGCAGCTACACCTACCCCCAAGCTCCCTGGGCCACGCAGTCGTTGATGG
GCAGATGGGCTTTCACAGTGACACCCTTAGCAAGGCCCCTGGGGTGAACAGCCTGAAGCAGGGCATGGTCAGCCTGAAAA
TTGGGGATGTCATCTCCTCTGCAGTCAAGACAGTGGGCTCTGTCATCAGCAGTGTGGCACTGATTGGCATCCTTTCTGGC
AATGATGGGACATATGTGAACATGGCAGTTTCAAAGCTGACCTCATGGGCTGCCATTGCCAGCAAGCCTGCAAAACCATG
GCCTAAAATGGAAACAAGGAGTGGGCCTGTCATAGGGGGGTGCACTGCCCCCTCCATCTATAAAGCATAACAAGGATATT
GACACCCAGTATAACAAGGGGCCTGTGCTGAAGACCCCGGTCCCCCAGGAGACATGATCCTCACAGGCTGTCCTACAACC
CCAGAAGGTGCTTCAGCTTCTCCCAATGAAGCTTCCTGCTTTGGCTCAACCACAGTATCAGAGCCCTCAGCAGCCACTCC
AGACCTGCTGGATCATTCCTCACGTGGAAATATGGCATTTGGGCAGAGCAGAGGGGTTGACAGTGGTAGTAACTCTCCTG
GAAATACCAAGACTAATTCTGCCCCAAGTGTAAAAAAAGTGAAAGCTGCCCACAGTTATAATCCTAAAGAATTTGACTGG
AATCTTAAAAGTGGACATGTACGCATTATAAAGAGCTATTCTGAGGATGACATTCACCACTCCATTAAGTACTCCCTTTT
GTGTAGTACAGAACATGGCACTACTTAGTTGAATAGTGCATTCAGCTCCATAAGCAGCAAGGGGCCTGTCTACCTGCTCT
TCGGCATCAGTGGGAGTGAGTATTTCTGTGGGGTGGCGGAGATGAAGTGCTCTGTGGACAGCAGCACCAGTGCCAGAGTC
TGGTCTCAAGACAAATGGAAGGGGAAGTTTGATGTCAAGTGGATTTTTGTCAGTGATGTACCCAATAACCAGCTCAGGCA
CATCAGACTGGAGAATCATGACAACAAGCCAGTCATAAACCATGAAACACAGGAGTTGCCTTTAGAAAAAGAAAAACAAG
TGCTGAAAATTATTGCTTCCTACAAGCACACAACCTCTATCTTTGATGACTTTTCTCACTACGCGAAATGCCAGGACGAG
GAGGAGGTGATGTGGAAGGAAAGACACAATCAAAATAAACAA

Alignment

ORF - retro_ptro_2170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.95 %
• Parental protein coverage: 99.28 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVDTQRTKGQDNKVQNGSLHQKDTVHDNDFEPYLTGQSNQSNSYPSMSDPYLSSYYPPSIGFPYSLNEAP
          S.DT.RTKG.D.KV.N.SLHQKD.VHDNDF.PYL.G.SN.SN.YPS.SD..LS.YYPPS.G.P.SLNEA.
Retrocopy SMDT*RTKGRDSKVHNDSLHQKDVVHDNDFQPYLSGESN*SNNYPSASDLCLSGYYPPSTGVP*SLNEAL

Parental  WSTAGDPPIPYLTTYGQLSNGDHHFMHDAVFGQPGGLGNNIYQHRFNFFPE-NPAFSAWGTSGSQGQQTQ
          WSTA.DP.I..L.TY.QLSN.DH.FMH....G.P.G..N.IYQHRFNF.P..NP.F.AW.TSGSQG.Q.Q
Retrocopy WSTARDPLILHLITYEQLSNRDHNFMHNSILGWPWGPENKIYQHRFNFYPQ<NPVFLAWRTSGSQG*QIQ

Parental  SSAYGSSYTYP-PSSLGGTVVDGQPGFHSDTLSKAPGMNSLEQGMVGLKIGDVSSSAVKTVGSVVSSVAL
          SS.YGSSYTYP.PSSLG..VVDGQ.GFHSDTLSKAPG.NSL.QGMV.LKIGDV.SSAVKTVGS.......
Retrocopy SSTYGSSYTYP<PSSLGHAVVDGQMGFHSDTLSKAPGVNSLKQGMVSLKIGDVISSAVKTVGSXXXXXXX

Parental  TGVLSGNGGTNVNMPVSKPTSWAAIASKPAKPQPKMKTKSGPVMGG-ALPPPPIKHNMDIGTWDNKGPVP
          ........GT.VNM.VSK.TSWAAIASKPAKP.PKM.T.SGPV.GG.ALPPP.IKHN.DI.T..NKGPV.
Retrocopy XXXXXXXDGTYVNMAVSKLTSWAAIASKPAKPWPKMETRSGPVIGG>ALPPPSIKHNKDIDTQYNKGPVL

Parental  KAPVPQQAPSPQAAPQPQQVAQPLPAQPPALAQPQYQSPQQPPQTRWVAPR-NRNAAFGQSGGAGSDSNS
          K.PVPQ...S.QA..QPQ.V.Q.LP...PALAQPQYQSPQQP.QT.W..P....N.AFGQS...G.DS..
Retrocopy KTPVPQET*SSQAVLQPQKVLQLLPMKLPALAQPQYQSPQQPLQTCWIIPH<RGNMAFGQS--RGVDS--

Parental  PGNVQPNSAPSVESHPVLEKLKAAHSYNPKEFEWNLKSGRVFIIKSYSEDDIHRSIKYSIWCSTEHGNKR
          .G...P.......S.P...K.KAAHSYNPKEF.WNLKSG.V.IIKSYSEDDIH.SIKYS..CSTEHG...
Retrocopy -GSNSPGNTKT-NSAPSVKKVKAAHSYNPKEFDWNLKSGHVRIIKSYSEDDIHHSIKYSLLCSTEHGTT*

Parental  LDSAFRCMSSKGPVYLLFSVNGSGHFCGVAEMKSPVDYGTSAGVWSQDKWKGKFDVQWIFVKDVPNNQLR
          L.SAF...SSKGPVYLLF...GS..FCGVAEMK..VD..TSA.VWSQDKWKGKFDV.WIFV.DVPNNQLR
Retrocopy LNSAFSSISSKGPVYLLFGISGSEYFCGVAEMKCSVDSSTSARVWSQDKWKGKFDVKWIFVSDVPNNQLR

Parental  HIRLENNDNKPVTNSRDTQEVPLEKAKQVLKIISSYKHTTSIFDDFAHYEKRQEEEEVVRKERQNRNKQ
          HIRLEN.DNKPV.N...TQE.PLEK.KQVLKII.SYKHTTSIFDDF.HY.K.Q.EEEV..KER.N.NKQ
Retrocopy HIRLENHDNKPVIN-HETQELPLEKEKQVLKIIASYKHTTSIFDDFSHYAKCQDEEEVMWKERHNQNKQ

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	0.02 RPM	41.95 RPM
SRP007412_cerebellum	0.00 RPM	67.75 RPM
SRP007412_heart	0.00 RPM	23.46 RPM
SRP007412_kidney	0.00 RPM	46.65 RPM
SRP007412_liver	0.00 RPM	44.52 RPM
SRP007412_testis	0.00 RPM	33.72 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2170 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2170 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2170 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3220
Gorilla gorilla	retro_ggor_2186

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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 ,