RetrogeneDB ID: retro_nleu_1672

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397303.1:6127821..6128901(-)
• Located in intron of: ENSNLEG00000002757

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNL3L
• Ensembl ID: ENSNLEG00000016233
• Aliases: None
• Description: None

Sequence

>retro_nleu_1672
GCTTTCAAGGCCAGGACCCAGCATCGGGTCAGCTTTGGAGCTGAAAACCTCATGAGGGTTCTGGGGAACTATTGCTGCCT
TGGTGAAGTGCGCACCCACATCCATATGGGCATTGGGGGCCTTCCCAATAATGGGAAGAGCAGCCTGATTAAAAGCCTGA
AGCGCAGCCATGCATGCAGTGTGGGAGCCATTCCTGGGGTCACGAAACTCATGCAGGAGATCTACCTGGACAAGTTCATC
TGGCTGCTGGATGCTCCAGCCATTGTTCCGGGGCCCAGCTCAGAGGTGGGCACCATCCTGCATAACTGCATCCACATCTA
GAGGCTGGCAGACCCCATGACCCTGGTGGAGACCATCTTGCAGTGCTGCAACCTGGAGGAGATTTCCAACTATTACCTTC
TTTCTGGGTACCGGACTACTGAGCACTTTCTGATGGCAGTGGCCCACCATTTGGGGAAGAAGAGAGACTTACACAGTCAG
GAGCAGGCAGCCAAAGCTGTCCTAGCTGACTGGGTGAGCGGGAAGATCAGCTTCTATAGACCACCACCACCCACTCACAC
TCTGCCCGCCCATCTCAGCGCTGAGATCATTAAGGAAATGACCAAGGTCTTCGACATCGAGGATACCGAGCAGGTCAATG
AAGACACCATGGAATGCTTGGCCACTGGAGAATCTGATGAGCTGTTGGGTGACACAGACCCACTCAAAATGGAGATCAAG
TTGCTCCATTCTCCGATGATGAAAATAGCAGATGCCATTGAAAATAAAGCTACCATGTATAAGATTGGAGATCTCACTGG
TTATTGCACCAATCCGAATCGTCATCAGATGGGGTGGGCTAAACTCAATGTAGACCACCACCCTAAAAAAAACAGTAAGG
TGGATGTGTGTCCAGTGGACTGCTGCCCAGTACTGCAGAGGATCATGGAGATGGACCCCCTACAACAGGGCCAGGCTCTG
GCATCCTCCCTGAAGAATAAGAATTTGCAGAAACGTGCAGATAAAATCCCCAGGGAGCTGTCTGATTCCATGATGTCTGC
CCTCCACCTCTCTGGCAATGCTGATGGCAGTGTTGGTGAC

Alignment

ORF - retro_nleu_1672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.61 %
• Parental protein coverage: 62.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASESLLKSKACFGAENLMRVLGNYCRLGEVRTHIRVGVVGLPNVGKSSLINSLKRSRACSVGAVPGITKF
          A..........FGAENLMRVLGNYC.LGEVRTHI..G..GLPN.GKSSLI.SLKRS.ACSVGA.PG.TK.
Retrocopy AFKARTQHRVSFGAENLMRVLGNYCCLGEVRTHIHMGIGGLPNNGKSSLIKSLKRSHACSVGAIPGVTKL

Parental  MQEVYLDKFIRLLDAPGIVPGPNSEVGTILRNCVHVQKLADPVTPVETILQRCNLEEISNYYGISGFQTT
          MQE.YLDKFI.LLDAP.IVPGP.SEVGTIL.NC.H...LADP.T.VETILQ.CNLEEISNYY..SG..TT
Retrocopy MQEIYLDKFIWLLDAPAIVPGPSSEVGTILHNCIHI*RLADPMTLVETILQCCNLEEISNYYLLSGYRTT

Parental  EHFLTAVAHRLGKKKKGGLYSQEQAAKAVLADWVSGKISFYIPPPATHTLPTHLSAEIVKEMTEVFDIED
          EHFL.AVAH.LGKK....L.SQEQAAKAVLADWVSGKISFY.PPP.THTLP.HLSAEI.KEMT.VFDIED
Retrocopy EHFLMAVAHHLGKKRD--LHSQEQAAKAVLADWVSGKISFYRPPPPTHTLPAHLSAEIIKEMTKVFDIED

Parental  TEQANEDTMECLATGESDELLGDTDPLEMEIKLLHSPMTKIADAIENKTTVYKIGDLTGYCTNPNRHQMG
          TEQ.NEDTMECLATGESDELLGDTDPL.MEIKLLHSPM.KIADAIENK.T.YKIGDLTGYCTNPNRHQMG
Retrocopy TEQVNEDTMECLATGESDELLGDTDPLKMEIKLLHSPMMKIADAIENKATMYKIGDLTGYCTNPNRHQMG

Parental  WAKRNVDHHPKSNNMVDVCSVDRRPVLQRIMETDPLQQGQALASALKNKKKMQKRADKIASKLSDSMMSA
          WAK.NVDHHP.....VDVC.VD..PVLQRIME.DPLQQGQALAS.LKN.K..QKRADKI...LSDSMMSA
Retrocopy WAKLNVDHHPXXXSKVDVCPVDCCPVLQRIMEMDPLQQGQALASSLKN-KNLQKRADKIPRELSDSMMSA

Parental  LNLSGNADDGVGD
          L.LSGNAD..VGD
Retrocopy LHLSGNADGSVGD

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_1672 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000252	2 retrocopies	retro_cjac_1591, retro_cjac_1853,
Homo sapiens	ENSG00000130119	1 retrocopy	retro_hsap_3327,
Gorilla gorilla	ENSGGOG00000007550	1 retrocopy	retro_ggor_1296,
Microcebus murinus	ENSMICG00000010144	1 retrocopy	retro_mmur_662,
Macaca mulatta	ENSMMUG00000008231	1 retrocopy	retro_mmul_2084,
Nomascus leucogenys	ENSNLEG00000016233	1 retrocopy	retro_nleu_1672 ,
Oryzias latipes	ENSORLG00000014117	1 retrocopy	retro_olat_29,
Pongo abelii	ENSPPYG00000020383	1 retrocopy	retro_pabe_2742,