RetrogeneDB ID: retro_nleu_782

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397273.1:11484821..11485897(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAF6
• Ensembl ID: ENSNLEG00000017949
• Aliases: None
• Description: None

Sequence

>retro_nleu_782
ATGAGTCTGCTAAACTGTGAAAACAGCTGTGGATCCAGCCAGTCTGAAGGTGACTACTGTGTGGCCATGGCCAGCTCCTG
TAGCGCTGCAACAAAAAATGATAGTGTGGGTGGAACTGCCAGCACGGGGAACCTCTCCAGCTCCTTTATGGAGGAGATTC
AGGGATATGATGTAGAGTTTGGCCCACCCCTGGAAAGCAACTATGAATGCCCCATCTGCTTGATGGCATTACGAGAAGCA
GTGCAAACGCCATGCAGCCATAGGTTCTGCAAAGCCTGCATCATAAAATCAATAAGGGATGCAGGTCACAAATGTCCAGT
TGACAATGAAATACTGCTGGAAAATAAACTATTTCCAGACAATTTTGCAAAACGTGAGATTCTTTCTCTGATAACGAAGT
GTCCAAATGAAGGTTATTTGCACAAAATGGAACTGAGACATCTTGAGGATCGTCACGCACATTGTGAGTTTGCTCTTATG
GATTGTCCCCAATGCCAGTGTCCCTTCCAAAAATTCCATATTAATATTCACATTCTGAAGGATTGTCCAAGGAGGCAGGT
ATCTTGTGACAATTGTGCTGCATCAATTGCATTTGAAGATAAAGAGATCCATGACCAGAACTGTCCTTTGACAAATGTCA
TCTGTGAGTACTGCAATACTATACTCATCAGAGAACAGATGCCTAACCTTATGACCTAGACTGCCCTACGGCCCCAATTC
CATGCATATTCAGTACTTTTGGTTGCCATGAAAAGATGCGGAGGAATCACTTGGCACGCCACCTACAAGAGAACACCCAG
TCAAACATAAGAATGTTGGCCCAGGCTGTTCACAGTTTGAGCCTTATACCCGACTCTGGGTATATCTCAGAGGTCCGGAA
TTTCCAGGAAACTATTCACCAATTAGAGGGTCGCCTTGTAAGACAAGATCATCAAATCTGGGAGCTGACTGATCAAATGG
AAACTCAGAGTATGTATGTAAGTGAGCTCAAACGAACCATTCGAACCCTTGAGGACAAAGTTGCTGAAGTTGAAGCATAG
CAGTGCAATGGAATTTACATTTGGAAGACTGGGAAT

Alignment

ORF - retro_nleu_782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.5 %
• Parental protein coverage: 68.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLLNCENSCGSSQSEGDCCVAMASSCSAATKDDSVGGTASTGNLSSSFMEEIQGYDVEFDPPLESKYEC
          MSLLNCENSCGSSQSEGD.CVAMASSCSAATK.DSVGGTASTGNLSSSFMEEIQGYDVEF.PPLES.YEC
Retrocopy MSLLNCENSCGSSQSEGDYCVAMASSCSAATKNDSVGGTASTGNLSSSFMEEIQGYDVEFGPPLESNYEC

Parental  PICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREILSLMVKCPNEGCL
          PICLMALREAVQTPC.HRFCKACIIKSIRDAGHKCPVDNEILLEN.LFPDNFAKREILSL..KCPNEG.L
Retrocopy PICLMALREAVQTPCSHRFCKACIIKSIRDAGHKCPVDNEILLENKLFPDNFAKREILSLITKCPNEGYL

Parental  HKMELRHLEDHQAHCEFALMDCPQCHRPFQKFHINIHILKDCPRRQVSCDNCAASMAFEDKEIHDQNCPL
          HKMELRHLED..AHCEFALMDCPQC..PFQKFHINIHILKDCPRRQVSCDNCAAS.AFEDKEIHDQNCPL
Retrocopy HKMELRHLEDRHAHCEFALMDCPQCQCPFQKFHINIHILKDCPRRQVSCDNCAASIAFEDKEIHDQNCPL

Parental  ANVICEYCNTILIREQMPN-HYDLDCPTAPIPCTFSTFGCHEKMQRNHLARHLQENTQSHMRMLAQAVHS
          .NVICEYCNTILIREQMPN..YDLDCPTAPIPC.FSTFGCHEKM.RNHLARHLQENTQS..RMLAQAVHS
Retrocopy TNVICEYCNTILIREQMPN<PYDLDCPTAPIPCIFSTFGCHEKMRRNHLARHLQENTQSNIRMLAQAVHS

Parental  LSLIPDSGYISEVRNFQETIHQLEGRLVRQDHQIRELTAKMETQSMYVSELKRTIRTLEDKVAEIEAQQC
          LSLIPDSGYISEVRNFQETIHQLEGRLVRQDHQI.ELT..METQSMYVSELKRTIRTLEDKVAE.EA.QC
Retrocopy LSLIPDSGYISEVRNFQETIHQLEGRLVRQDHQIWELTDQMETQSMYVSELKRTIRTLEDKVAEVEA*QC

Parental  NGIYIWKIGN
          NGIYIWK.GN
Retrocopy NGIYIWKTGN

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_782 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000036009	1 retrocopy	retro_btau_391,
Homo sapiens	ENSG00000175104	1 retrocopy	retro_hsap_680,
Gorilla gorilla	ENSGGOG00000005854	1 retrocopy	retro_ggor_586,
Nomascus leucogenys	ENSNLEG00000017949	1 retrocopy	retro_nleu_782 ,
Pan troglodytes	ENSPTRG00000003510	1 retrocopy	retro_ptro_488,