RetrogeneDB ID: retro_nleu_2875

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397457.1:2329457..2330437(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARG2
• Ensembl ID: ENSNLEG00000000741
• Aliases: None
• Description: None

Sequence

>retro_nleu_2875
AGTCTGGTTGTGATAGGAGCCCTGTTCTTGTAGGGACAGAAAAGAAAAGGAGTGGAACACGGTCCAGCTGCCAGAAGAAA
AATTGGATTGATGAAAAGGTCTCCAATTTGGGCTGCTGCCTAAAAGGCTTTGGAAATTTTAGTTTTACTCCAGTCCCCAC
AGATGAGCTCTTCAACAATCCAACAGTGAATCTGTGCCAAGTGGCCCAGCCAACCAGCAACAGGCTGAGCTGGTTAGCAG
AGCAGTGTTGTCTGGCTACAGCCGTGTCACAGTGAGAGGAGACCACAGCCTGGCAATTAGTACCATTAGTGGCCATGCCT
GAAACTGCCCAGACCTTTGTGTCACTTGGGTTGATGCCCAGCAGACATCAGTACACCCCTTACCACTTCATCAGGAAATC
TCCATGGACCATCAGTTTCATTTCTCCTCAGAGAACTACAGGGAAAGGTACCAGAACTTCCAGGATTTCCCTGGACAAAC
CTTGTATGTCTTCCCCAAGTACAGTGTATTCTAGTCTAGGAGATGCGGACCCTCTGGAACATTTTTTTTAAAAGAACAAC
GATATCTAGTATTTTTCCATGAGAGACATTGATCCACTTGGTACCCAGAAGGTCATGCAAGAGAAATTTGATCTGCTGAT
TAGGAAAAGACAAAGGTCCGTCCATCTGAGTTTTCATATCCATGTATTTGACTCTACACTGGCTGCAGCCACAGGAATCC
CTATTGTAGGGGGACGGACCTTTCAAGAAGGCATCTATATTGCTGAGGAAATACATAGTACAGGGTTGCTGTCAGCACTG
GATCTTGTTGAAGTCAATCCTCAACCAGGTACTTCAGAGGAAGGGGTAAAGGCCACAGCTAGCTTGCCAGTAGATGTAAC
TGCTTTACGTTTGGGTCAGACAAGGGAAGGAGGGCACATTGCCTATGGCCAGATTTTCAGTTTCCCAGCCAAGTCAGAAA
ATGAAGCATGTGTGAGAATT

Alignment

ORF - retro_nleu_2875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.66 %
• Parental protein coverage: 93.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVAVIGAPFSQGQKRKGVEHGPAAIREAGLLKR-LSSLGCHLKDFGDLSFTPVPKDDLYNNLIVNPRSV-
          S..VIGA.F..GQKRKGVEHGPAA.R..GL.KR..S.LGC.LK.FG..SFTPVP.D.L.NN..VN...V.
Retrocopy SLVVIGALFL*GQKRKGVEHGPAARRKIGLMKR<VSNLGCCLKGFGNFSFTPVPTDELFNNPTVNLCQV<

Parental  GLANHELAEVVSRAVSDGYSCVTLGGDHSLAIGTISGHARHCPDLCVVWVDAH-ADINTPLTTSSGNLHG
          G.AN...AE.VSRAV..GYS.VT..GDHSLAI.TISGHA..CPDLCV.WVDA..ADI.TPLTTSSGNLHG
Retrocopy GPANQQQAELVSRAVLSGYSRVTVRGDHSLAISTISGHA*NCPDLCVTWVDAQ<ADISTPLTTSSGNLHG

Parental  QPVSFLLRELQDKVPELPGFSWI-KPCISTASIVYIGLRDVDPPEHFILKNYDIQYFSMRDIDRLGIQKV
          ..VSFLLRELQ.KVPELPGF.W..KPC.S..S.VY..L.D.DP.E....KN.DI.YFSMRDID.LG.QKV
Retrocopy PSVSFLLRELQGKVPELPGFPWT<KPCMSSPSTVYSSLGDADPLEXXXXKNNDI*YFSMRDIDPLGTQKV

Parental  TERTFDLLIGKRQRPIHLSFDIDAFDPTLAPATGSPVVGGLTYREGMYIAEEIYNTGLLSALDLVEVNPQ
          ....FDLLI.KRQR..HLSF.I..FD.TLA.ATG.P.VGG.T..EG.YIAEEI..TGLLSALDLVEVNPQ
Retrocopy MQEKFDLLIRKRQRSVHLSFHIHVFDSTLAAATGIPIVGGRTFQEGIYIAEEIHSTGLLSALDLVEVNPQ

Parental  LATSEEEAKTTANLAVDVIASSFGQTREGGHIVYDQLPTPSSPDESGNQAHVRI
          ..TSEE..K.TA.L.VDV.A...GQTREGGHI.Y.Q....S.P..S.N.A.VRI
Retrocopy PGTSEEGVKATASLPVDVTALRLGQTREGGHIAYGQI--FSFPAKSENEACVRI

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_2875 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005722	1 retrocopy	retro_acar_91,
Choloepus hoffmanni	ENSCHOG00000007159	1 retrocopy	retro_chof_1179,
Callithrix jacchus	ENSCJAG00000015277	4 retrocopies	retro_cjac_1933, retro_cjac_2357, retro_cjac_2561, retro_cjac_902,
Dasypus novemcinctus	ENSDNOG00000004808	1 retrocopy	retro_dnov_251,
Homo sapiens	ENSG00000081181	1 retrocopy	retro_hsap_3501,
Gorilla gorilla	ENSGGOG00000005615	1 retrocopy	retro_ggor_2367,
Monodelphis domestica	ENSMODG00000009978	1 retrocopy	retro_mdom_257,
Nomascus leucogenys	ENSNLEG00000000741	2 retrocopies	retro_nleu_2875 , retro_nleu_792,
Oryctolagus cuniculus	ENSOCUG00000000584	1 retrocopy	retro_ocun_277,
Pongo abelii	ENSPPYG00000005926	1 retrocopy	retro_pabe_2893,
Pan troglodytes	ENSPTRG00000006467	1 retrocopy	retro_ptro_2373,