RetrogeneDB ID: retro_nleu_2496

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397362.1:1352014..1354835(+)
• Located in intron of: ENSNLEG00000016160

Retrocopy information

• Ensembl ID: ENSNLEG00000016210
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OFD1
• Ensembl ID: ENSNLEG00000009180
• Aliases: None
• Description: None

Sequence

>retro_nleu_2496
ATGATGGCTCAGTCCAACATGCTCCCTGTGGCTGACATGTTGAGTCAAAATGAACTGCGCAAAAAGCTATACCAGACATT
TAAGGATCGGGGTATACTGGACACACTCAAGACACAACTTCGAAACCAGCTAATTCATGAGTTAATGCACCCTGTATTGA
GTGGAGAACTGCAACCTCGGTCCATTTCAGTGCAAGGGAGCTCCCTCTTAATAAGCGCCTCTAACTCTTTAGTGGCAGAT
CACTTACAAAGATGTGGCTATGAATATTCACTTTCTGTTTTCTTTCCAGAAAGTGGTTTGGCAAAAGAAAAGGTATTTAC
TATGCAGGATCTATTACAACTCATTAAAATCAACCCTACTTCCAGTCTCTACAAATCACTGGTTTCAGGAGCTGATAAAG
AAAACCAAAAAGGTTTTCTTATGCATTTTTTAAAAGAATTGGCAGAATATCATCAAGCTAAAGAGAGTTGTAATATGGGA
ACTCAGACAAGTTTGACATTTAGCAGAGATTCTCTGGCTGAGAAGCTTCAGCTTATTGATGATCAGTTTGCAGATGCTTA
CCCTCAGTGTATCAAGTTCGAGTCTTTAGAAATAAAGCTAAATGAATATAAGAGAGAAATAGAAGAGCAACTTCAGGCAG
AAATATGTCAAAAGTTGAAGTTTTTTAAAGATACCGAAATAGGAAAAATTAAAATGGAAGCAAAAAAAAAGTATGAGAAG
AAATTAGCCGTGTTCCAGAATGATTTTGAGAAAGCTTGTCAAGCAAAATCTGAAGCCCTCGTTATTCGGGAAAAGAGCAC
CCTTGAGAGAATTCAAAAGCACCAAGAGATTGAAACAAAAGAAATTTATGCTCAAAGGCAACTTTTACTAAAAGATATGG
ATTTGCTAAGAGGAAGAGAAGCAGAGCTGAAGCAAAGAGTTGAAGCTTTTGAACTGAACCAGAAGCTCCAGGAAGAAAAA
CATAAAAGCATGACTGAGGCACTTAGGAGACGGGAGCAGAATATAAAGAGTTTTGAGAAGACCTATGACCAAAAACTGAA
GAATGAACTTCTAAAGTATCAACTTGAACTAAAGGACGACTACATCATTAGAACTAATCGACTGATTGAAGATGAAAGGA
AGAATAAAGAAAAAGCTGTTCATTTGCAAGAGGAGCTCATAGCTTTTAATTCAAAAAAGGAGGAACTCAATCAATCTATA
AATCGCATGAAAGAACTTGAGCTTGAGTTAGAGTCTGTCAAAGCCCAGTCTTTGGCAATAACAAAACAAAACCATATGCT
GAATGAAAAGGTTAAAGTGATGAGTGATTATTCACCACTAAAAGAAGAGAGACTGGAGCTTCTGGCACAAAATAAATTAC
TTAAACAACAACTGGAAGAGAGTAGAAATGAAAACTTGCGTCTCCTAAACCGCCTAGCTCAGCCGGCTCCTGAACTTGCG
GTCTTTCAGAAAGAACTACAGAAAGCAGAAAAGGCTTTAGTGGTTGAGCATGAGGAGTTCAAAAGCCGCAGGCAAGCTCT
GCACAAACAACTGCAAGATGAAATTGAGCATACTACACAGTTGAAGGCCCAGATACTAGCTTACAAAGCTTCCATAAAGA
GGTTAACTATTCAGGTTGCTGATTTAAAATCGCAACTGAAGCAAACTCAGACAGCCCTAGAGAATGAAGTGTACTGCAAT
CCAAAGCAGTCTGTGATCCATCATTCTGCCAATGGATTAATAAATGGCAACATGGTGCTTCACAATGGTGAGATAAGTGG
GGGATTTCCTTGAACAATCCTTCTAAACAGGAAAATGTTCTAGCAGGTATGGTTGCATCAAGGATCACAAATTATCCAAA
TGCAGGGATGGAGGGTAGTTCCCCTGATCTGACCTTGAGTTTGTTGCCAATACTAATGCAAGGGTCAAAGAGCTTCAGCA
AGAGGCCGAACGCTTGGAAAAGGCTTTCAGAAGTTACCATCGGAGAGACATTAAAAACTCTGCCAAAGGCCCACTACCAG
CAAAGAGCCCACCATCTCTGCATTTGCTGGAAGCCTTCAAAAACATTACTTCCAGTTCCCCGGAAAGACGTATTTTTGCA
GAGGACAGAGTTGTCTCTGAGCAGCCTCAAGTGGGCACATTTAAAGAAGAAAGGAATGACATCTTGGAAGCCCTGACAGG
CAGTGCAGCCTCAAGGCTACGCGGGAGCACTTCCTCCAGATGCCTCTCCTCCACACCCCTTCCAAAAGCAAAAAGAAGCC
TTGAAAGTGAAATATATCTGGAAGGTCTGGGCAGATCACACGTTGCTTCCCCCAGTCCTTGTCCTGACAGAATGCCCCCG
CCATCACCCACTGAGTCTAGGCACAACCTCTCCATCCCTCCCTTCTCCAGCCCTCCGGAGAAGAAAGCGGGTCTTTATTG
GAGACAAAATGAACTTCAAGACAAAAGTGAATTTTCAGATGTGGACAAGCTAGCTTTTAAGGATAACGAGGAATTTGAAT
CATCTTTTGAATATGCAGGGAATGTGCCAAAGCAGTTTGAAATGGATGGGCCCGCTCCTGCCGGGGATATGCTTCATATG
GGCGCAGCTGTAGGTGCTGTGCCCCTCTCATATCAGCACCCAAGTGTAGATCAGAAGCAAATTGAAGAACAAAAGGAAGA
AGAAAAAATATGGGAACAGCAAGTGAAAGAACAAAAGCACAGAAAAGAAAGAAGGCAGAGTAACCTACAAGAAATTTTAG
AAACGGAAAGAAGAGAGCTAGAAAAACTGTATCAGGAAAGGAGGATGACCGAAGAATCACTGAAGATTGAAATGGAAAAT
GAATTAGAAATGAGTAATCAA

Alignment

ORF - retro_nleu_2496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.93 %
• Parental protein coverage: 92.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MMAQSNMLPVADVLSQDELRKKLYQTFKDRGILDTLKTQLRNQLIHELMHPVLSGELQPRSISVEGSSLL
          MMAQSNMLPVAD.LSQ.ELRKKLYQTFKDRGILDTLKTQLRNQLIHELMHPVLSGELQPRSISV.GSSLL
Retrocopy MMAQSNMLPVADMLSQNELRKKLYQTFKDRGILDTLKTQLRNQLIHELMHPVLSGELQPRSISVQGSSLL

Parental  IGASNSLVADHLQRCGYEYSLSVFFPESGLAKEKVFTMQDLLQLIKINPTSSLYKSLVSGSDKENQKGFL
          I.ASNSLVADHLQRCGYEYSLSVFFPESGLAKEKVFTMQDLLQLIKINPTSSLYKSLVSG.DKENQKGFL
Retrocopy ISASNSLVADHLQRCGYEYSLSVFFPESGLAKEKVFTMQDLLQLIKINPTSSLYKSLVSGADKENQKGFL

Parental  MHFLKELAEYHQAKESCNMETQTSSTFNRDSLAEKLQLIDDQFADAYPQRIKFESLEIKLNEYKREIEEQ
          MHFLKELAEYHQAKESCNM.TQTS.TF.RDSLAEKLQLIDDQFADAYPQ.IKFESLEIKLNEYKREIEEQ
Retrocopy MHFLKELAEYHQAKESCNMGTQTSLTFSRDSLAEKLQLIDDQFADAYPQCIKFESLEIKLNEYKREIEEQ

Parental  LRAEMCQKLKFFKDTEVAKIKTEAKKKYEKELAMFQNDFEKACQAKSEALVLREKSTLERIQKHQEIETK
          L.AE.CQKLKFFKDTE..KIK.E....YEK.LA.FQNDFEKACQAKSEALV.REKSTLERIQKHQEIETK
Retrocopy LQAEICQKLKFFKDTEIGKIKMEXXXXYEKKLAVFQNDFEKACQAKSEALVIREKSTLERIQKHQEIETK

Parental  EIYAQRQLLLKDMDLLRGREAELKQRVEAFELNQKLQEEKHKSITEALRRREQNIKSFEETYDRKLKNEL
          EIYAQRQLLLKDMDLLRGREAELKQRVEAFELNQKLQEEKHKS.TEALRRREQNIKSFE.TYD.KLKNEL
Retrocopy EIYAQRQLLLKDMDLLRGREAELKQRVEAFELNQKLQEEKHKSMTEALRRREQNIKSFEKTYDQKLKNEL

Parental  LKYQLELKDDYIIRTNRLIEDERKNKEKAVHLQEELIAINSKKEELNQSVNRVKELELELESVKAQSLAI
          LKYQLELKDDYIIRTNRLIEDERKNKEKAVHLQEELIA.NSKKEELNQS.NR.KELELELESVKAQSLAI
Retrocopy LKYQLELKDDYIIRTNRLIEDERKNKEKAVHLQEELIAFNSKKEELNQSINRMKELELELESVKAQSLAI

Parental  TKQNHMLNEKVKEMSDYSLLKEEKLELLAQNKLLKQQLEESRNENLHLLNRLAQPAPELAVFQKELQKAE
          TKQNHMLNEKVK.MSDYS.LKEE.LELLAQNKLLKQQLEESRNENL.LLNRLAQPAPELAVFQKELQKAE
Retrocopy TKQNHMLNEKVKVMSDYSPLKEERLELLAQNKLLKQQLEESRNENLRLLNRLAQPAPELAVFQKELQKAE

Parental  KAIVVEHEEFESRRQALHKQLQDEIEHSAQLKAQILSYKASVKRLTTQVADLKLQLKQTQTALENEVYCN
          KA.VVEHEEF.SRRQALHKQLQDEIEH..QLKAQIL.YKAS.KRLT.QVADLK.QLKQTQTALENEVYCN
Retrocopy KALVVEHEEFKSRRQALHKQLQDEIEHTTQLKAQILAYKASIKRLTIQVADLKSQLKQTQTALENEVYCN

Parental  PKQSVIDRSVNGLINGNVVPCNGEIS-GDFL-NNPFKQENVLARMVASRITNYPNAWVEGSSPD-SDLEF
          PKQSVI..S.NGLINGN.V..NGEIS.GDFL.NNP.KQENVLA.MVASRITNYPNA..EGSSPD.SDLEF
Retrocopy PKQSVIHHSANGLINGNMVLHNGEIS>GDFL>NNPSKQENVLAGMVASRITNYPNAGMEGSSPD<SDLEF

Parental  VANTKARVKELQQEAERLEKAFTSYHRRVIKNSAKSPLAAKSPPSLHLLEAFKNITSSSPERHIFGEDRV
          VANT.ARVKELQQEAERLEKAF.SYHRR.IKNSAK.PL.AKSPPSLHLLEAFKNITSSSPER.IF.EDRV
Retrocopy VANTNARVKELQQEAERLEKAFRSYHRRDIKNSAKGPLPAKSPPSLHLLEAFKNITSSSPERRIFAEDRV

Parental  VSEQPQVGTL-EERNDILEALTGSAASRLRGGTSSRRLSSTPLPKAKRSLESEMYLEGVGRSHVASPSPC
          VSEQPQVGT..EERNDILEALTGSAASRLRG.TSSR.LSSTPLPKAKRSLESE.YLEG.GRSHVASPSPC
Retrocopy VSEQPQVGTFKEERNDILEALTGSAASRLRGSTSSRCLSSTPLPKAKRSLESEIYLEGLGRSHVASPSPC

Parental  PDRMPLPSPTESRHSLSIPPVSSPPEQKVGLYRRQTELQDKSEFSDVDKLAFKDNEEFESSFESAGNVPR
          PDRMP.PSPTESRH.LSIPP.SSPPE.K.GLY.RQ.ELQDKSEFSDVDKLAFKDNEEFESSFE.AGNVP.
Retrocopy PDRMPPPSPTESRHNLSIPPFSSPPEKKAGLYWRQNELQDKSEFSDVDKLAFKDNEEFESSFEYAGNVPK

Parental  QLEMGGLSPAGDMPHVDAAAAAVPLSYQHPSVDQKQIEEQKEEEKIREQQVNERRQREERRQSNLQEVLE
          Q.EM.G..PAGDM.H..AA..AVPLSYQHPSVDQKQIEEQKEEEKI.EQQV.E...R.ERRQSNLQE.LE
Retrocopy QFEMDGPAPAGDMLHMGAAVGAVPLSYQHPSVDQKQIEEQKEEEKIWEQQVKEQKHRKERRQSNLQEILE

Parental  RERRELEKLYQERRMIEESLKIEIENELEMENE
          .ERRELEKLYQERRM.EESLKIE.ENELEM.N.
Retrocopy TERRELEKLYQERRMTEESLKIEMENELEMSNQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2496 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,