RetrogeneDB ID: retro_nleu_856

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397275.1:13659410..13660140(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNT1
• Ensembl ID: ENSNLEG00000003226
• Aliases: None
• Description: None

Sequence

>retro_nleu_856
AATAAGAAACTCAAGAGCTACCACTTAGCACAGGTTGAACTTTCCTCTTAATATTCTTCCCAACTAAGCTAGACCTTCCT
ACACTTTTATGGGACAATTGTAGAGGAAACTGGTGACCATGATCCTGAAACTTTGTAAACAATTGCAGAAAATGCAAAAC
GCTTGGGTGGAATATCAGGAATGAGGATTTGGGTGGAACTGAAAAAATGTTTGTTGGTAACCATGTAAATCATTTGATTC
CCCTTATCTGTGATCTTGATGTGGCTCCTTACGTAGATTTATCTGCTAATTAAAGTTTAGAAGAGTTTAATAAGGTCAGA
AAAAATGTTGAAGGTTTTTCACCAAAGTCAATGACTCTTTTTGCCTCATTATTCAAGTGATAGGATGATGTTGCAAAAGT
GGATTTGAGGTCGACGACTGCACAAAAAGAGAAAAGTCTTGGATTATTTATGGTTAAAAATAGGAAAGATTTAATTAAAG
CAACAGATAGTTCAGAACCATTGAAACTCTATCAAGACTTCATTACAGCTTCTAGGGAACATGATGCAACTACTTGTGTA
TGTGAGCTACTGAGGTACCCAGGAGAGCACTGTCTCTGAAAGGAAATGCAGCAACGGAGAATCCCATTTCCTGTAACTGT
CATGACATCAGGAAAGTGGGGATCTCTTCAGGGAAAGAAATTGGGGCTCTATTACAACAGCTGTGAGAACAGTGGGAAAA
AAGTGGTTTC

Alignment

ORF - retro_nleu_856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.85 %
• Parental protein coverage: 55.99 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKKVRFVGHAKQRIQEDYLRILR--YFRFYGRIVDKPGDHDPETLEAIAENAKGLAGISGERIWVELKKI
          NKK......A.......Y...L......FYG.IV...GDHDPETL..IAENAK.L.GISG.RIWVELKK.
Retrocopy NKKLKSYHLAQVELSS*YSSQLS*TFLHFYGTIVEETGDHDPETL*TIAENAKRLGGISGMRIWVELKKC

Parental  L-VGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVEGFSPKPMTLLASLFKVQDDVTKLDLRLK
          L.VGNHVNHLI.LI.DLDVAPY..L.AN.SLEEF.KV.KNVEGFSPK.MTL.ASLFK..DDV.K.DLR..
Retrocopy L<VGNHVNHLIPLICDLDVAPYVDLSAN*SLEEFNKVRKNVEGFSPKSMTLFASLFK**DDVAKVDLRST

Parental  IAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSIP
          .A..EK.LGLF.VKNRKDLIKATDSS.PLK.YQDFI..SRE.DATT.VCELL.Y.GEHCL.KEMQQ..I.
Retrocopy TAQKEKSLGLFMVKNRKDLIKATDSSEPLKLYQDFITASREHDATTCVCELLRYPGEHCL*KEMQQRRI-

Parental  PFPV-SGHDIRKVGISSGKEIGALLQQLREQWKKSGY
          PFPV...HDIRKVGISSGKEIGALLQQL.EQW.KSG.
Retrocopy PFPV<NCHDIRKVGISSGKEIGALLQQL*EQWEKSGF

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_856 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015466	1 retrocopy	retro_cjac_1512,
Dasypus novemcinctus	ENSDNOG00000008837	1 retrocopy	retro_dnov_1635,
Echinops telfairi	ENSETEG00000018177	2 retrocopies	retro_etel_1871, retro_etel_905,
Homo sapiens	ENSG00000072756	2 retrocopies	retro_hsap_246, retro_hsap_2598,
Gorilla gorilla	ENSGGOG00000015286	1 retrocopy	retro_ggor_300,
Nomascus leucogenys	ENSNLEG00000003226	1 retrocopy	retro_nleu_856 ,
Petromyzon marinus	ENSPMAG00000002236	1 retrocopy	retro_pmar_17,
Pongo abelii	ENSPPYG00000013702	3 retrocopies	retro_pabe_1916, retro_pabe_2721, retro_pabe_412,
Pan troglodytes	ENSPTRG00000014564	1 retrocopy	retro_ptro_1522,