RetrogeneDB ID: retro_nleu_804

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397273.1:7234741..7235608(-)
• Located in intron of: ENSNLEG00000012049

Retrocopy information

• Ensembl ID: ENSNLEG00000012073
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TATDN1
• Ensembl ID: ENSNLEG00000005467
• Aliases: None
• Description: None

Sequence

>retro_nleu_804
ATGAGTCATTTCAAGTTTATCGATATTGGTATCAAATTGACTGACCCCATGTTCATAGGAATTTATAGGGGGGTTCAAAA
GCATCAAGATGACTTACAGAATGTAATAGGGAGAGCTGTCGAGATTGGTGTTAAAAAGTTTATGATTACAGGTGGAAATC
TACAAGACAGTAAAGATGCACCGCATTTGGCACAAACAAATCATATGTTTTTCAGTACAGTTGGATGTCATCCTACAAGA
TGTGGTGAATTTGAAAATAACCCTGATCTTTACTTAAAGGAGTTGCTAAATCTTGCTGAAAACAATAAAGGGAAAGTTGT
GGCAATAGGAGAATGTGGACTTGATTTTGACCGACTGCAGTTTTGTCCCAAAGATACTCAACTCAAATATTTTAAAAAAT
AGTTTGAACTGTCAGAACAAACAATATTACCAATGTTTCTTCATTGTCGAAACTCACATGCTGAATTTTTGGACATAATG
AAAAGAAATAGAGATCGGTGTGTAGGGGGAGTGGTGCATTCATTTGATGGTACCAAGGAAGGAGCAGCTGCTTTGATTGA
CTTGGATCTTTATATAGGATTTAATGGTTGCTCACTGAAAACTGAAACTAATTTGAAAGTTTTGAAGTCAATTCCTAGTG
AAAAATTAATGATTGAGACAGATGCACCTTGGTGTGGAGTCAAAAGTACACATGCTGGATCAAAATATATAAAAACTGCA
TTTCCTACCAAAAAGAAGTGGAAAAGTGGGCACTGCTGAAAAGACAGAAATGAACCCTGCCATATAATTCAAATATTGGA
GATAATGTCAGCAGTGAGAGATGAGGATCCACTGGAATCAGCCAATACACTATATAACAATACTATT

Alignment

ORF - retro_nleu_804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.48 %
• Parental protein coverage: 97.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRFKFIDIGINLTDPMFRGIYRGVQKHQDDLQDVIGRAVEIGVKKFMITGGNLQDSKDALHLAQTNDMF
          MS.FKFIDIGI.LTDPMF.GIYRGVQKHQDDLQ.VIGRAVEIGVKKFMITGGNLQDSKDA.HLAQTN.MF
Retrocopy MSHFKFIDIGIKLTDPMFIGIYRGVQKHQDDLQNVIGRAVEIGVKKFMITGGNLQDSKDAPHLAQTNHMF

Parental  FSTVGCHPTRCGEFEKNNPDLYLKELLNLAENNKGKVVAIGECGLDFDRLQFCPKDTQLKYFEKQFELSE
          FSTVGCHPTRCGEFE.NNPDLYLKELLNLAENNKGKVVAIGECGLDFDRLQFCPKDTQLKYF.K.FELSE
Retrocopy FSTVGCHPTRCGEFE-NNPDLYLKELLNLAENNKGKVVAIGECGLDFDRLQFCPKDTQLKYFKK*FELSE

Parental  QTKLPMFLHCRNSHAEFLDIMKRNRDRCVGGVVHSFDGTKEAAAALIDLDLYIGFNGCSLKTEANLEVLK
          QT.LPMFLHCRNSHAEFLDIMKRNRDRCVGGVVHSFDGTKE.AAALIDLDLYIGFNGCSLKTE.NL.VLK
Retrocopy QTILPMFLHCRNSHAEFLDIMKRNRDRCVGGVVHSFDGTKEGAAALIDLDLYIGFNGCSLKTETNLKVLK

Parental  SIPSEKLMIETDAPWCGVKSTHAGSKYIKTAFPTKKKWESGHCLKDRNEPCHIIQILEIMSAVRDEDPLE
          SIPSEKLMIETDAPWCGVKSTHAGSKYIKTAFPTKKKW.SGHC.KDRNEPCHIIQILEIMSAVRDEDPLE
Retrocopy SIPSEKLMIETDAPWCGVKSTHAGSKYIKTAFPTKKKWKSGHC*KDRNEPCHIIQILEIMSAVRDEDPLE

Parental  LANTLYNNTI
          .ANTLYNNTI
Retrocopy SANTLYNNTI

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_804 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033446	1 retrocopy	retro_btau_463,
Homo sapiens	ENSG00000147687	1 retrocopy	retro_hsap_578,
Gorilla gorilla	ENSGGOG00000015875	1 retrocopy	retro_ggor_514,
Nomascus leucogenys	ENSNLEG00000005467	1 retrocopy	retro_nleu_804 ,
Oryctolagus cuniculus	ENSOCUG00000017403	1 retrocopy	retro_ocun_730,
Rattus norvegicus	ENSRNOG00000047198	1 retrocopy	retro_rnor_1737,
Tupaia belangeri	ENSTBEG00000006179	1 retrocopy	retro_tbel_707,