RetrogeneDB ID: retro_nleu_2382

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397350.1:3908964..3909555(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: U2AF1
• Ensembl ID: ENSNLEG00000014737
• Aliases: None
• Description: U2 small nuclear RNA auxiliary factor 1 [Source:HGNC Symbol;Acc:12453]

Sequence

>retro_nleu_2382
CAGACAATTGCCCTCTTAAACATTTACTGTAACCCTCAAAACTCTTCCCAGTCGGCGGACGGTTTGCGTTGTGCCGTGAG
CGATGTTGAGATGCAGGAACACTATGATGAATTTTTTGAGGAGGTTTTCATAGAATTGGAGGAGAAGTATGGGGAAGTTG
AGGAGATGAACGTCTGTGACAACCTGGGAGACCACCTGGTGGGGAACGTGTAAGTCAAGCTTTGCCCTGAGGAAGATGCG
GAAAAGGCTGTGATTGACTTGAACAACCGTTGGTTTAACGGACAGCCGATCCACGCCGAGCTGTCACCTGTGACGGACTT
CAGGGGAGCCAGCTGCCGTCAGTATGAGATGGGAGAATGCACACGAGGCGGCTTCTGCAACTTCATGCATTTGAAGCCCA
TTTCCAGAGAGCTGCGGCGGAAGCTGTGTGGGCAGCGTCGCAAGAAGCACAGATGAAGATCCCGATCCCGGGAGCGTCGT
TCTCGGTCTAGAGACCGTGGTTGTGGCGGTGGCGGTGGCAGTGGCCCAGGCGGCGGCGGACGGGAGCGTGACAGGAGGCA
GTTGAGAGATCGTGAAAGATCTGGGCGATTC

Alignment

ORF - retro_nleu_2382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.31 %
• Parental protein coverage: 83.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QTILIQNIYRNPQNSAQTADGSHCAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNV
          QTI...NIY.NPQNS.Q.ADG..CAVSDVEMQEHYDEFFEEVF.E.EEKYGEVEEMNVCDNLGDHLVGNV
Retrocopy QTIALLNIYCNPQNSSQSADGLRCAVSDVEMQEHYDEFFEEVFIELEEKYGEVEEMNVCDNLGDHLVGNV

Parental  YVKFRREEDAEKAVIDLNNRWFNGQPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPISRELRR
          .VK...EEDAEKAVIDLNNRWFNGQPIHAELSPVTDFR.A.CRQYEMGECTRGGFCNFMHLKPISRELRR
Retrocopy *VKLCPEEDAEKAVIDLNNRWFNGQPIHAELSPVTDFRGASCRQYEMGECTRGGFCNFMHLKPISRELRR

Parental  ELYGRRRKKHRSRSRSRERRSRSRDRGRGGGGGGGGGGGGRERDRRRSRDRERSGRF
          .L.G.RRKKHR.RSRSRERRSRSRDRG.GGGGG.G.GGGGRERDRR..RDRERSGRF
Retrocopy KLCGQRRKKHR*RSRSRERRSRSRDRGCGGGGGSGPGGGGRERDRRQLRDRERSGRF

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_2382 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015558	1 retrocopy	retro_ecab_1081,
Homo sapiens	ENSG00000160201	2 retrocopies	retro_hsap_1478, retro_hsap_790,
Loxodonta africana	ENSLAFG00000011460	1 retrocopy	retro_lafr_1135,
Macaca mulatta	ENSMMUG00000022769	2 retrocopies	retro_mmul_1071, retro_mmul_2126,
Mus musculus	ENSMUSG00000061613	3 retrocopies	retro_mmus_1602, retro_mmus_1787, retro_mmus_2955,
Nomascus leucogenys	ENSNLEG00000009496	1 retrocopy	retro_nleu_1,
Nomascus leucogenys	ENSNLEG00000014737	1 retrocopy	retro_nleu_2382 ,
Otolemur garnettii	ENSOGAG00000016504	1 retrocopy	retro_ogar_241,
Pongo abelii	ENSPPYG00000011463	2 retrocopies	retro_pabe_1227, retro_pabe_703,