RetrogeneDB ID: retro_nleu_2800

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397435.1:281399..282394(-)
• Located in intron of: ENSNLEG00000013158

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSFL1C
• Ensembl ID: ENSNLEG00000009341
• Aliases: None
• Description: NSFL1 (p97) cofactor (p47) [Source:HGNC Symbol;Acc:15912]

Sequence

>retro_nleu_2800
CAGATTGCGCTAGCGAGCTTTTATGACACAGAGAAAGAAGACATCATAACCATTTCACAGGCAACCTCCCGTTCAGTGTC
CAGAGGCACAGCCCCTAGTGATAATAGAGTGACATCCTTTAGAGACTTCACTCATGACCAAGATGAGGATGAGGAAGAGG
AGGAAGGCCAGAGGTTTCATGCTGGGGCCTCAGAGAGAAGTGGACAGCAGACTGTTGGCCCTCCCAGAAAGAAAAGTCCC
AATGAGCTGGTGGATGATCTCTTTAAAGGTGCCAAAGAGCATGGAGCTGTAGCTGTGGAGCGAGTGACCAAGAGACCTGG
AGAGACCAGTACACCAAGACCATTTGCAGGAGGTGGCTATGGCCTTGGGACAGCACCAGAGGAAGAGTCTGCTTATGTGA
CAGGAGAAAAGAGACAGCATTCCAGCCAAGATGTTCATGTAGTACTGAAACTCTGCAAGAGTGGATTCAGCCTGGATAAT
GGAGAACTCAGAAGCTACTGAGACCCATCCAATGCCCAGTTTCTGGAGTCTATCCACAGAGGGGAGGTGCCAGCAGAGCT
GTGGAGGCTAGCTCACAGTGGACAAGCGAACTTGGATATGGAGGCCATCAGGACGAGGACTTTATGAAGTCCAAATAAGC
CTTCAAAGCCTTCACTGGCGAGGGTCAGAAACTGAGCAGCACTGCCCTCTAGGTGTTGAGTACCATCTCTCCAGTCCAAC
TGGCAGAAAATGAAGCCAAAGCCAGCTCTTCCATCTTAATCGTCGAATCAGAGACTACCACAAACATCCAAATTCGGCTT
GCAGACGGTGTGAGGCTGGTGCAGAAATTTAACCACAGCCACAGGATCAGCAACATCCAACTCTTCATTGTGGATGCCCG
GCCAGCCATGGCTGCCACCAGCTTTATCCTCATGACTACTTTCCCAAACAAAGAGCTGGCTGATGAGAGCTGGACCCTGA
AGGAAGCCAACCTGCTCAATGCTGCCATCATGCAG

Alignment

ORF - retro_nleu_2800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.83 %
• Parental protein coverage: 96.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QIALASFYEDGGDEDIVTISQATPSSVSRGTAPSDNRVTSFRDLIHDQDEDEEEEEGQRFYAGGSERSGQ
          QIALASFY.D...EDI.TISQAT..SVSRGTAPSDNRVTSFRD..HDQDEDEEEEEGQRF.AG.SERSGQ
Retrocopy QIALASFY-DTEKEDIITISQATSRSVSRGTAPSDNRVTSFRDFTHDQDEDEEEEEGQRFHAGASERSGQ

Parental  QIVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAGGGYRLGAAPEEESAYVAGEKRQ
          Q.VGPPRKKSPNELVDDLFKGAKEHGAVAVERVTK.PGETS.PRPFAGGGY.LG.APEEESAYV.GEKRQ
Retrocopy QTVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKRPGETSTPRPFAGGGYGLGTAPEEESAYVTGEKRQ

Parental  HSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLESIRRGEVPAELRRLAHGGQVNLDME-DHRDEDF
          HSSQDVHVVLKL.KSGFSLDNGELRSY.DPSNAQFLESI.RGEVPAEL.RLAH.GQ.NLDME..H.DEDF
Retrocopy HSSQDVHVVLKLCKSGFSLDNGELRSY*DPSNAQFLESIHRGEVPAELWRLAHSGQANLDME<GHQDEDF

Parental  VKPKGAFRAFTGEGQKLGSTAPQVLSTSSPAQQAENEAKASSSILIDESEPTTNIQIRLADGGRLVQKFN
          .K.K.AF.AFTGEGQKL.STA..VLST.SP.Q.AENEAKASSSILI.ESE.TTNIQIRLADG.RLVQKFN
Retrocopy MKSK*AFKAFTGEGQKLSSTAL*VLSTISPVQLAENEAKASSSILIVESETTTNIQIRLADGVRLVQKFN

Parental  HSHRISDIRLFIVDARPAMAATSFILMTTFPNKELADESQTLKEANLLNAVIVQ
          HSHRIS.I.LFIVDARPAMAATSFILMTTFPNKELADES.TLKEANLLNA.I.Q
Retrocopy HSHRISNIQLFIVDARPAMAATSFILMTTFPNKELADESWTLKEANLLNAAIMQ

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_2800 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000088833	1 retrocopy	retro_hsap_4050,
Gorilla gorilla	ENSGGOG00000013539	1 retrocopy	retro_ggor_2718,
Macropus eugenii	ENSMEUG00000003940	2 retrocopies	retro_meug_1890, retro_meug_605,
Macaca mulatta	ENSMMUG00000015994	1 retrocopy	retro_mmul_2337,
Mus musculus	ENSMUSG00000027455	1 retrocopy	retro_mmus_2565,
Nomascus leucogenys	ENSNLEG00000000751	1 retrocopy	retro_nleu_2612,
Nomascus leucogenys	ENSNLEG00000001356	1 retrocopy	retro_nleu_2984,
Nomascus leucogenys	ENSNLEG00000009341	1 retrocopy	retro_nleu_2800 ,
Otolemur garnettii	ENSOGAG00000002630	2 retrocopies	retro_ogar_1144, retro_ogar_1609,
Pongo abelii	ENSPPYG00000010851	1 retrocopy	retro_pabe_3324,
Pan troglodytes	ENSPTRG00000013164	1 retrocopy	retro_ptro_2745,