RetrogeneDB ID: retro_ptro_2274

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:77937558..77940573(-)
• Located in intron of: ENSPTRG00000023298

Retrocopy information

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

Parental gene information

• Parental gene symbol: OFD1
• Ensembl ID: ENSPTRG00000021675
• Aliases: None
• Description: oral-facial-digital syndrome 1 [Source:HGNC Symbol;Acc:2567]

Sequence

>retro_ptro_2274
ATGATGGCTCAGTCCAACATGCTCCCCGTGGCTGATGTGTTGAGTCAAAATGAACTGCGCAAAAAGCTATACCAGACATT
TAAGGATCGGGGTATACTGGACACACTCAAGATACAACTTCGAAACCAGCTAATTCATGAGTTAATGCACCCTGTATTTA
GTGGAGAACTGCAACCTCAGTCCATTTCAGTGCAAGGGAGCTCCCTCTTAATAAGTGCCTCTAACTCTTTAGTGGCAGAT
CACTTACAAAGATGTGGCTATGAATATTCACTTTCTGTTTTCTTTCTAGAAACTGGTTTGGCAAAAGAAAAGGTATTTAC
TATGCAGGATCTATTACAACTCATTAAAATCAACCCTACTTCCAGTCTGTACAAATCACTGGTTTCAGGAGCTGATAAAG
AAAACCAAAAAGGTTTTCTTATGCATTTTTTAAAAGGATTGGCAGAATATCATCAAGCTAAAGAGAGTTGTAATATGGAA
ACTCAGACAAGTTCAACATTTAGCAGAGATTCTCTGGCTGAGAAGCTTCAGCTTATTGATGATCAGTTTGCAGATGCTTA
CCCTCAGCGTATCAAGTTCGAGTCTTTAGAAATAAAGCTAAATGAATATAAGAGAGAAATAGAAGAGCAACTTCGGGAAG
AAATATGTCAAAAGTTGAAGTTTTTTAAAGATACCGAAATAGGAAAAATTAAAATGGAAGCAAAAAAAAAGTATGAGAAG
GAATTAGCCGTGTTCCAGAATGATTTTGAGAAAGCTTGTCAAGCAAAATCTGAAGCCCTTGTTATTCGGGAAAAGAGCAC
CCTTGAGAGAATTCAAAAGCACCAAGAGATTGAAACAAAAGAGATTTATGCTCAAAGGCAACTTTTACTAAAAGATATGG
ATTTGCTAAGAGGAAGAGAAGCAGAGCTGAAGCAAAGAGTTGAAGCTTTTGAACTGAACCAGAAGCTCCAGGAAGAAAAA
CATAAAAGTATGACTGAGGCACTTAGGAGACGGGAGCAGAATATAAAGAGTTTTGAGAGGACCTATGACCAAAAACTCAA
GAATGAACTTCTAAAGTATCAACTTGAACTAAAGGACGACTACATCATTAGAACTAATCGACTGATTGAAGATGAAAGGA
AGAATAAAGAAAAAGCTGTTCATTTGCAAGAGGAGCTCATAGCTTTTAATTCAAAAAAGGAGGAACTCAATCAATCTATA
AATCGCATGAAAGAACTTGAGCTTGAATTAGAGTCTGTCAAAGCCCAGTCTTTGGCAATAACAAAACAAAACCATATGCT
GAATGAAAAGGTTAAAGTGATGAGTGACTATTCACTACTAAAAGAAGAGAGACTGGAGCTTCTGGCACAAAATAAATTAC
TTAAACAACAACTGGAAGAGAGTAGAAATGAAAACTTGCGTCTCCTAAACCGCCTAGCTCAGCTGGCTCCTGAACTTGCG
GTCTTTCAGAAAGAACTACGGAGAGCAGAAAAGGCTACAGTGGTTGAGCATGAGGAGTTCGAAAGCCGCAAACAAGCTCT
GCACAAACAACTGCAAGATGAAATTGAGCATACTACACAGTTGAAGGCCCAGATACTAGGTTACAAAGTTTCCATAAAGA
GGTTAACTATTCAGGTTGCCGATTTAAAATCGCAACTGAAGCAAACTCAGACAGCCCTAGAGAATGAAGTGTACTGCAAT
CCAAAGCAGTCTGTGATCCATCATTCTGCCAATGGATTAATAAATGGCAACATGGTGCTTCACAATGGCGAGATAAGTGG
GGATTTCTTGAACAATCCTTTTAAACAGGAAAAAGTTCTAGCAGGTATGGTTGCATCAAGGATCACAAATTATCCAAATG
CAGGGATGGAGGGTAGTTCCCCTGATTCTGACCTTGAGTTTGTCGCCAATACTAATGCAAGGGTCAAACAGCTTCAGCAA
GAGGCGGAACGCTTGGAAAAGGCTTTCAGAAGTTACCATCGGAGAGACATTAAAAACTCTGCCAAAGGCCCACTACCAGC
AAAGAGCCCACCATCTCTGCACTTGCTGGAAGCCTTCAAAAACATTACTTCCAGTTCCCCGGAAAGACGTATTTTTGCAG
AGGACAGAGTTGTCTCTGAGCAGCCTCAAGTGGGCACACTTAAAGAAGAAAGGAATGACATCTTGGAAGCCCTGACAGGC
AGTGCAGCCTCAAGGCTACGCGGGGGCACTTCCTCCAGACGCCTCTCCTCCACACCCCTTCCAAAAGCAAAAAGAAGCCT
TGAAAGTGAAATATATCTGGAAGGTCTGGGCAGATCACACATTGCTTCCCCCAGTCCTTGTCCTGACAGAATGCCCCCGC
CATCACCCGCTGAGTCTAGGCACAACCTCTCCATCCCTCCCTTCTCCAGCCCTCCGGAGCAGAAAGCGGGTCTTTATTGG
AGACAAAATGAACTTCAAGACAAAAGTGAATTTTCAGATGCGGACAAGCTAGCTTTTAAGGATAACGAGGAATTTGAATC
ATCTTTTGAATATGCACAGAATGTGCCAAGGCAGTTTGAAATGGATGGGCCCTCTCCTGCCGGGGATATGCTTCATATGG
GCGCAGCTGTAGCTGCTGTGCCCCTCTCATATCAGCACCCAAGTGTAGATCAGAAACAAATTGAAGAACAAAAGGAAGAA
GAAAAAATATGGGAACAGCAAGTGAAAGAACGAAAGCAGAGAGAAGAAAGAAGGCAGAGTAACCTACAAGAAATTTTAGA
AAGGGAAAGAAGAGAACTAGAAAAACTGTATCAGGAAAGGAGGATGACTGAAGAATCACTGAAGATTGAAATGGAAAATG
AATTAGAAATGAGTAATCAAGAAATGAAAGACAAATCTGCTCACAGTGAAAATCCTTTAGAGAAATACATGAAAATCATC
CAGCAAGACCAGGAGTCGGCAGATAAGAGCTCAAAAAAGATGGTCCAGGAAGGCTCCCTAGTGGACACACTGCAATGTAG
TGACAAAGTTGAAAGTTTAACACGCTTTTCTCATGAAGAACCAGATGACTCTTGG

Alignment

ORF - retro_ptro_2274 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMAQSNMFTVADVLSQDELRKKLYQTFKDRGILDTLKTQLRNQLIHELMHPVLSGELQPRSISVEGSSLL
          MMAQSNM..VADVLSQ.ELRKKLYQTFKDRGILDTLK.QLRNQLIHELMHPV.SGELQP.SISV.GSSLL
Retrocopy MMAQSNMLPVADVLSQNELRKKLYQTFKDRGILDTLKIQLRNQLIHELMHPVFSGELQPQSISVQGSSLL

Parental  IGASNSLVADHLQRCGYEYSLSVFFPESGLAKEKVFTMQDLLQLIKINPTSSLYKSLVSGSDKENQKGFL
          I.ASNSLVADHLQRCGYEYSLSVFF.E.GLAKEKVFTMQDLLQLIKINPTSSLYKSLVSG.DKENQKGFL
Retrocopy ISASNSLVADHLQRCGYEYSLSVFFLETGLAKEKVFTMQDLLQLIKINPTSSLYKSLVSGADKENQKGFL

Parental  MHFLKELAEYHQAKESCNMETQTSSTFNRDSLAEKLQLIDDQFADAYPQRIKFESLEIKLNEYKREIEEQ
          MHFLK.LAEYHQAKESCNMETQTSSTF.RDSLAEKLQLIDDQFADAYPQRIKFESLEIKLNEYKREIEEQ
Retrocopy MHFLKGLAEYHQAKESCNMETQTSSTFSRDSLAEKLQLIDDQFADAYPQRIKFESLEIKLNEYKREIEEQ

Parental  LRAEMCQKLKFFKDTEIAKIKMEAKKKYEKELTMFQNDFEKACQAKSEALVLREKSTLERIHKHQEIETK
          LR.E.CQKLKFFKDTEI.KIKME....YEKEL..FQNDFEKACQAKSEALV.REKSTLERI.KHQEIETK
Retrocopy LREEICQKLKFFKDTEIGKIKMEXXXXYEKELAVFQNDFEKACQAKSEALVIREKSTLERIQKHQEIETK

Parental  EIYAQRQLLLKDMDLLRRREAELKQRVEAFELNQKLQEEKHKSITEALRRQEQNIKSFEETYDRKLKNEL
          EIYAQRQLLLKDMDLLR.REAELKQRVEAFELNQKLQEEKHKS.TEALRR.EQNIKSFE.TYD.KLKNEL
Retrocopy EIYAQRQLLLKDMDLLRGREAELKQRVEAFELNQKLQEEKHKSMTEALRRREQNIKSFERTYDQKLKNEL

Parental  LKYQLELKDDYIIRTNRLIEDERKNKEKAVHLQEELIAINSKKEELNQSVNRVKELELELESVKAQSLAI
          LKYQLELKDDYIIRTNRLIEDERKNKEKAVHLQEELIA.NSKKEELNQS.NR.KELELELESVKAQSLAI
Retrocopy LKYQLELKDDYIIRTNRLIEDERKNKEKAVHLQEELIAFNSKKEELNQSINRMKELELELESVKAQSLAI

Parental  TKQNHMLNEKVKEMSDYSLLKEEKLELLAQNKLLKQQLEESRNENLRLLNRLAQPAPELAVFQKELRKAE
          TKQNHMLNEKVK.MSDYSLLKEE.LELLAQNKLLKQQLEESRNENLRLLNRLAQ.APELAVFQKELR.AE
Retrocopy TKQNHMLNEKVKVMSDYSLLKEERLELLAQNKLLKQQLEESRNENLRLLNRLAQLAPELAVFQKELRRAE

Parental  KAIVVEHEEFESRRQALHKQLQDEIEHSAQLKAQILGYKASVKSLTTQVADLKLQLKQTQTALENEVYCN
          KA.VVEHEEFESR.QALHKQLQDEIEH..QLKAQILGYK.S.K.LT.QVADLK.QLKQTQTALENEVYCN
Retrocopy KATVVEHEEFESRKQALHKQLQDEIEHTTQLKAQILGYKVSIKRLTIQVADLKSQLKQTQTALENEVYCN

Parental  PKQSVIDRSVNGLINGNVVPCNGEISGDFLNNPFKQENVLARMVASRITNYPTAWVEGSSPDSELEFVAN
          PKQSVI..S.NGLINGN.V..NGEISGDFLNNPFKQE.VLA.MVASRITNYP.A..EGSSPDS.LEFVAN
Retrocopy PKQSVIHHSANGLINGNMVLHNGEISGDFLNNPFKQEKVLAGMVASRITNYPNAGMEGSSPDSDLEFVAN

Parental  TKARVKELQQEAERLEKAFRSYHRRVIKNSAKSPLAAKSPPSLHLLEAFKNITSSSPERHIFGEDRVVSE
          T.ARVK.LQQEAERLEKAFRSYHRR.IKNSAK.PL.AKSPPSLHLLEAFKNITSSSPER.IF.EDRVVSE
Retrocopy TNARVKQLQQEAERLEKAFRSYHRRDIKNSAKGPLPAKSPPSLHLLEAFKNITSSSPERRIFAEDRVVSE

Parental  QPQVGTL-EERNDVVEALTGSAASRLRGGTSSRRLSSTPLPKAKRSLESEMYLGGLGRSHIASPSPCPDR
          QPQVGTL.EERND..EALTGSAASRLRGGTSSRRLSSTPLPKAKRSLESE.YL.GLGRSHIASPSPCPDR
Retrocopy QPQVGTLKEERNDILEALTGSAASRLRGGTSSRRLSSTPLPKAKRSLESEIYLEGLGRSHIASPSPCPDR

Parental  MPLPSPTESRHSLSIPPVSSPPEQKVGLYRRQTELQDKSEFSDVDKLAFKDNEEFESSFESAGNVPRQLE
          MP.PSP.ESRH.LSIPP.SSPPEQK.GLY.RQ.ELQDKSEFSD.DKLAFKDNEEFESSFE.A.NVPRQ.E
Retrocopy MPPPSPAESRHNLSIPPFSSPPEQKAGLYWRQNELQDKSEFSDADKLAFKDNEEFESSFEYAQNVPRQFE

Parental  MGGLSPAGDMSHVDAAAAAVPLSYQHPSVDQKQIEEQKEEEKIREQQVKERRQREERRQSNLQEVLERER
          M.G.SPAGDM.H..AA.AAVPLSYQHPSVDQKQIEEQKEEEKI.EQQVKER.QREERRQSNLQE.LERER
Retrocopy MDGPSPAGDMLHMGAAVAAVPLSYQHPSVDQKQIEEQKEEEKIWEQQVKERKQREERRQSNLQEILERER

Parental  RELEKLYQERKMIEESLKIKIKKELEMENELEMSNQEIKDKSAHSENPLEYMKIIQQEQDHSADKSSKKM
          RELEKLYQER.M.EESLKI....ELEM.N..EM............E.........Q...D.S.....KKM
Retrocopy RELEKLYQERRMTEESLKIEMENELEMSNQ-EMKDKSAHSENP-LEKYMKIIQQDQESADKSS----KKM

Parental  VQEGSLVDTLQSSDKVESLTGFSHEELDDSW
          VQEGSLVDTLQ.SDKVESLT.FSHEE.DDSW
Retrocopy VQEGSLVDTLQCSDKVESLTRFSHEEPDDSW

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	0.07 RPM	12.99 RPM
SRP007412_cerebellum	0.39 RPM	13.26 RPM
SRP007412_heart	0.20 RPM	7.00 RPM
SRP007412_kidney	0.42 RPM	26.99 RPM
SRP007412_liver	0.33 RPM	13.55 RPM
SRP007412_testis	4.32 RPM	58.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2274 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2274 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3164
Gorilla gorilla	retro_ggor_1352

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003979	1 retrocopy	retro_cjac_2845,
Callithrix jacchus	ENSCJAG00000035427	1 retrocopy	retro_cjac_2844,
Homo sapiens	ENSG00000046651	1 retrocopy	retro_hsap_3164,
Gorilla gorilla	ENSGGOG00000006453	1 retrocopy	retro_ggor_1352,
Nomascus leucogenys	ENSNLEG00000009180	1 retrocopy	retro_nleu_2496,
Pan troglodytes	ENSPTRG00000021675	1 retrocopy	retro_ptro_2274 ,