RetrogeneDB ID: retro_nleu_1016

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:24091108..24092045(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR82
• Ensembl ID: ENSNLEG00000007104
• Aliases: None
• Description: None

Sequence

>retro_nleu_1016
ATGAAGCTGACCCACTGTGTGCTGCTGCGGAGCTTCTTTATCGTCAACGTGTTCTGCGAAAACTCGGACAAGATTAACTG
CTTCGATTTCAGCCCTAACAGCGGGGTGATCACTTCGAGCAGCAACGATGACTCTATCATGCTCTATGACTGCCAGGAGG
ACAAACCAAAACCCTGTTCAGTAAGAAATACGGTGTGGCCTCATCAGATACAGTCCTGCGGCAAACACAGTTGTTTACAG
CTCTAACAAAATAGACGATACTATTCGTTATTTGTCCTTGCATGACAACAAATATATCAGATACTTTCCTGGACATAGCA
AAAGGGTGGTGGTCTTGTCCATGTCACCTGTGGATGACACTTTCATTTCTGGGTCTCTTGAATAAGACCATTCGACTCTG
GGATCTCTCGTCTCCCAACTGCCAGGGCCTCATGCATATAAAGGGGAAGCCAGTTTGTTCTTTTGATCCAGAAGGGGGAA
TTTTTGCTGCTGGTGTCAACTCTGAAATGGTCAAACTTTATGACCTTCGTTCTTTTGATAAGGGGCCATTTGCTACCTTT
AAGATGCAGTATGATCAAACTTGTGACTGGACAGCACTTAAAATCAGCAACGGTGGCAAGCTCATCCTCATTTCCACCAA
TGTCAGCTTCATTCGTCTCATTGGTGCATTCAAAGGAGTGGTGAGACACACATTTGGCAGTTATGCCAACAGCAAAGCTG
TCACACTGGAGGCTTCATTTACTGCAGACTCTCAGTTTGTTATTATGGTTCAGAGGATGGCAAGATCCATTTCTGGAATG
GAGAGAGTGGTATAAAAGTAGCTGTGTTGGATGGTAGACACACAGGCCCAATTACCTGTTTGCAATTCAACCCCAAGTTT
GTGACTTTTGCCAGCGGGTGTACCAACATGGCCTTTGGGTTGCCCACCGTTGATGAC

Alignment

ORF - retro_nleu_1016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MKLTDSVL-RSFRVAKVFRENSDKINCFDFSPNGETVISSSDDDSIVLYDCQE-GKPKRTLYSKKYGV-D
          MKLT..VL.RSF....VF.ENSDKINCFDFSPN.....SSS.DDSI.LYDCQE.G..K.TL.SKKYGV..
Retrocopy MKLTHCVLLRSFFIVNVFCENSDKINCFDFSPNSGVITSSSNDDSIMLYDCQE<GQTK-TLFSKKYGV<G

Parental  LIRYTHAANTVVYSSNKIDDTIRYLSLHDNKYIRYFPGHSKRVVALSMSPVDDTFISGSLD-KTIRLWDL
          LIRY..AANTVVYSSNKIDDTIRYLSLHDNKYIRYFPGHSKRVV.LSMSPVDDTFISGSL..KTIRLWDL
Retrocopy LIRYSPAANTVVYSSNKIDDTIRYLSLHDNKYIRYFPGHSKRVVVLSMSPVDDTFISGSLE>KTIRLWDL

Parental  RSPNCQGLMHLQGKPVCSFDPEGLIFAAGVNSEMVKLYDLRSFDKGPFATFKMQYDRTCEWTGLKFSNDG
          .SPNCQGLMH..GKPVCSFDPEG.IFAAGVNSEMVKLYDLRSFDKGPFATFKMQYD.TC.WT.LK.SN.G
Retrocopy SSPNCQGLMHIKGKPVCSFDPEGGIFAAGVNSEMVKLYDLRSFDKGPFATFKMQYDQTCDWTALKISNGG

Parental  KLILISTNGSFIRLIDAFKGVVMHTFGGYANSKAVTLEASFTPDSQFIMI-GSEDGKIHVWNGESGIKVA
          KLILISTN.SFIRLI.AFKGVV.HTFG.YANSKAVTLEASFT.DSQF....GSEDGKIH.WNGESGIKVA
Retrocopy KLILISTNVSFIRLIGAFKGVVRHTFGSYANSKAVTLEASFTADSQFVIM<GSEDGKIHFWNGESGIKVA

Parental  VLDGKHTGPITCLQFNPKFMTFASACSNMAFWLPTIDD
          VLDG.HTGPITCLQFNPKF.TFAS.C.NMAF.LPT.DD
Retrocopy VLDGRHTGPITCLQFNPKFVTFASGCTNMAFGLPTVDD

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_1016 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000774	1 retrocopy	retro_chof_2299,
Callithrix jacchus	ENSCJAG00000006114	1 retrocopy	retro_cjac_3022,
Homo sapiens	ENSG00000164091	2 retrocopies	retro_hsap_2816, retro_hsap_419,
Loxodonta africana	ENSLAFG00000028309	1 retrocopy	retro_lafr_639,
Macropus eugenii	ENSMEUG00000009280	1 retrocopy	retro_meug_1207,
Macaca mulatta	ENSMMUG00000008234	2 retrocopies	retro_mmul_339, retro_mmul_511,
Monodelphis domestica	ENSMODG00000011614	4 retrocopies	retro_mdom_1259, retro_mdom_144, retro_mdom_219, retro_mdom_398,
Nomascus leucogenys	ENSNLEG00000007104	2 retrocopies	retro_nleu_1016 , retro_nleu_1195,
Otolemur garnettii	ENSOGAG00000016032	1 retrocopy	retro_ogar_1314,
Pongo abelii	ENSPPYG00000013812	2 retrocopies	retro_pabe_185, retro_pabe_300,
Rattus norvegicus	ENSRNOG00000048441	3 retrocopies	retro_rnor_1003, retro_rnor_1109, retro_rnor_1152,