RetrogeneDB ID: retro_nleu_1473

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397295.1:5734910..5736537(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2H1
• Ensembl ID: ENSNLEG00000017760
• Aliases: None
• Description: None

Sequence

>retro_nleu_1473
ATGGCAACTTCCTCTGAAGAAGTTTCGCTGATTGTAAAGAAAGTGCGTCAAAAGAAGCAGGATGGAGCTCTATACCTCAT
GGCAGAAAGAATTGCTTGGGCACCTGAAGGCAAAAATGGATTTACAATCAGCCATATGTATGTGGTTATTAAATGCCAGG
AAATTAGTCCAGGAGGAAAAGCTAAAATTCAGCATCAGCTGGACCTATATGCAGGAGATACAATTAACTTCCATTTTTCC
AGTGAAAACACAGCAGTGAAAGAGCAAGATGCAGTAAAGGACCTTCTTCAGCAGCTGCTGCCCAAATTCAAGAGGAAAGC
AAATAAAGAACTGGAAGAGAAGAACAGAATGCTGCAAAAAGATCCTGTTTTGTTTCAGCTTTATAAAGACCTTGTTGTGA
GCCAAGTGATGAGCGCTGAGGAATTCTGGGCCAATCGTTTAAATGTGAATGCAACAGAAAATTCTTCCACATCCGATCAT
AAGCAGGATATTGACATTTCTGCTGCATTTCTGGCTGATGTCTGGCCCCAAACCGATGGCTGTAACGGTCTGAGATATAA
TTTAACTCCTGAAATCATTGAGTTCATATTTAGGACCTACCCAGCAGTAAAAATGAAATATGCAGGAAATGTTCCCCACA
ACATGACAGAGAAGGGATTCTAGACACGTTTTTTCCAGTCCCATTATTTTCACAGGGATCGGCTGAATACAGGGTCAAAG
GATCTCTTTGCAGAATGTGACAAAATAGATGAAAAAGGCCTAAAAACAATGGTTTCATTAGGAGTGAAAAACCCACTACT
AGAATTAACAGCTTTGGGAGATAAACCATTAGATGAGGGCTATGGCATTTCCTCTGTGCCATCTGCTTCCAATTCTAAAT
CCATAAAAGAGAATAGTAATGCTGCCATCAAGAGATTTAACCATCACATTGCCATGGTCCTGGCAGCTGGACTCAGGAAA
CAAGAAGCAGAAAATGAACAAAATAGCCCAGCAGCATGGATGGAAATTCCAGAGATGCAGACTGCTTTCAGCCAATAGTC
AAAAGGGTGAAATCACAAGAGTCCAGTGAATATGAAGACTTGGGGAAAAATAATTCTGTAAAAATGATTGCACTAAACAT
CAAGAAGTCAGATAGGCATTATCATGGTCCAACTCCAATCCAGTCACTACAGTATGCGACAAGTCAGGACATTATTCTTT
TCAAAGTATTGGGTAAGAAATGGAAGCTTATACACCCAAGTTAACTGAGGTTCTCTTGAGTAGTGCTGCCAGTAGTACCA
TCACAGCACTGTCACCTGGAGGGGCACTTATGCAGGGAGGAACACAGCAAACCATAAACCAGATGGTGCCAAGTGATATT
CAGTCTGAATTGAAACACTTGTATGTAGCTACTGGAGAACTTCTACAGCATTTCTGGTCCTGCTTTCCTGTTAATATACA
ATTCCTAGGAGAAAAGGTAGTGAAAATGAAAAGTAACTTGGAACGATTCCAAGTTACGAAGCTCTGCCCATTCCAAGAAA
AGATTCGGAGACAGTATTTAAGCCCACATTTGGTAAGTCACATAGAGATACTCCAGGCAGCCTACAACAAGCTCCACACA
TGGCAGTCATGGTGTCTGATGAAAGAA

Alignment

ORF - retro_nleu_1473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.79 %
• Parental protein coverage: 99.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLH
          MATSSEEV.LIVKKVRQKKQDGALYLMAERIAWAPEGK..FTISHMY..IKCQ.ISP.GKAKIQ.QL.L.
Retrocopy MATSSEEVSLIVKKVRQKKQDGALYLMAERIAWAPEGKNGFTISHMYVVIKCQEISPGGKAKIQHQLDLY

Parental  AGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDLVVSQVISAE
          AGDT.NFHFS.E.TAVKE.DAVKDLLQQLLPKFKRKANKELEEKNRMLQ.DPVLFQLYKDLVVSQV.SAE
Retrocopy AGDTINFHFSSENTAVKEQDAVKDLLQQLLPKFKRKANKELEEKNRMLQKDPVLFQLYKDLVVSQVMSAE

Parental  EFWANRLNVNATDSSSTSNHKQDVGISAAFLADVRPQTDGCNGLRYNLTSDIIESIFRTYPAVKMKYAEN
          EFWANRLNVNAT..SSTS.HKQD..ISAAFLADV.PQTDGCNGLRYNLT..IIE.IFRTYPAVKMKYA.N
Retrocopy EFWANRLNVNATENSSTSDHKQDIDISAAFLADVWPQTDGCNGLRYNLTPEIIEFIFRTYPAVKMKYAGN

Parental  VPHNMTEKEFWTRFFQSHYFHRDRLNTGSKDLFAECAKIDEKGLKTMVSLGVKNPLLDLTALEDKPLDEG
          VPHNMTEK.F.TRFFQSHYFHRDRLNTGSKDLFAEC.KIDEKGLKTMVSLGVKNPLL.LTAL.DKPLDEG
Retrocopy VPHNMTEKGF*TRFFQSHYFHRDRLNTGSKDLFAECDKIDEKGLKTMVSLGVKNPLLELTALGDKPLDEG

Parental  YGISSVPSASNSKSIKENSNAAIIKRFNHHSAMVLAAGLRKQETQNEQNSEPS-NMDGNSGDADCFQPAV
          YGISSVPSASNSKSIKENSNAA.IKRFNHH.AMVLAAGLRKQE..NEQNS.P...MDGNS.DADCFQP.V
Retrocopy YGISSVPSASNSKSIKENSNAA-IKRFNHHIAMVLAAGLRKQEAENEQNS-PA<SMDGNSRDADCFQPIV

Parental  KRAKLQESIEYEDLGKNNSVKTIALNLKKSDRYYHGPTPIQSLQYATSQDIINSFQSIRQEMEAYTP-KL
          KR.K.QES.EYEDLGKNNSVK.IALN.KKSDR.YHGPTPIQSLQYATSQDII..F...........P.KL
Retrocopy KRVKSQESSEYEDLGKNNSVKMIALNIKKSDRHYHGPTPIQSLQYATSQDII-LFKVLGKKWKLIHP<KL

Parental  TQVLSSSAASSTITALSPGGALMQGGTQQAINQMVPNDIQSELKHLYVAVGELLRHFWSCFPVNTPFLEE
          T.VL.SSAASSTITALSPGGALMQGGTQQ.INQMVP.DIQSELKHLYVA.GELL.HFWSCFPVN..FL.E
Retrocopy TEVLLSSAASSTITALSPGGALMQGGTQQTINQMVPSDIQSELKHLYVATGELLQHFWSCFPVNIQFLGE

Parental  KVVKMKSNLERFQVTKLCPFQEKIRRQYLSTNLVSHIEEMLQTAYNKLHTWQSRRLMKK
          KVVKMKSNLERFQVTKLCPFQEKIRRQYLS..LVSHI.E.LQ.AYNKLHTWQS..LMK.
Retrocopy KVVKMKSNLERFQVTKLCPFQEKIRRQYLSPHLVSHI-EILQAAYNKLHTWQSWCLMKE

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_1473 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
Homo sapiens	ENSG00000110768	1 retrocopy	retro_hsap_1892,
Gorilla gorilla	ENSGGOG00000008405	1 retrocopy	retro_ggor_1385,
Monodelphis domestica	ENSMODG00000006540	1 retrocopy	retro_mdom_1210,
Nomascus leucogenys	ENSNLEG00000017760	1 retrocopy	retro_nleu_1473 ,
Otolemur garnettii	ENSOGAG00000000710	1 retrocopy	retro_ogar_338,
Pan troglodytes	ENSPTRG00000003420	1 retrocopy	retro_ptro_1269,