RetrogeneDB ID: retro_nleu_1595

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397300.1:13102709..13103271(-)
• Located in intron of: ENSNLEG00000004091

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD51AP1
• Ensembl ID: ENSNLEG00000003178
• Aliases: None
• Description: None

Sequence

>retro_nleu_1595
AATTACTCACAGTTTGGCGACTCTGACAGTGATGATGATTTTGTTTCTGCAACTGTACCTTTAAACAAGAAATCCAGAAC
ATCAAAGGAGTTAAAACAAGATAAACCAAAACCTAATTTGAACAATCTCCAGAAAGAAGAAATCCCACTGGAAGAGAAAA
CCCCTAAAAAAAAGGATGGCTTTAGATGACAAGCTCTACCAGAGAGACTTAGAAGTTGCACTAGCTTTATCAGTGAAGGA
ACTTTCAACAGTCACCACTAATGTGCAGAAGTCTCAAGATAAAAGAGTTGAAAAACATGGCAATAGTAGAACAGAAACAG
TGGGTAAGTCTCCTCATATCTCTAATTGCAGTGTAGCCAGTGATTATTTAGATTTGGATAAGATTACTGGGAAAGACAAT
GGTGGTATTCAAGGGAAAAGAAAAGCAGCATCTAAAGCTGCGGTACAACAGAGGAAAATTTTTCTGGAAGGCAGTGATGG
CAATAGTGCTAATGACACCAAACCAGACTTGGCAACTGGTGAAGATTCTGAGGACGATTCTGATTTTGGTGAGAGTGAGG
AC

Alignment

ORF - retro_nleu_1595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.68 %
• Parental protein coverage: 56.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NYSQFDHSDSDDDFVSATVPLNKKSRTALKELKQDKPKANLNNLQKEEIPVQEKAPKKR-MALDDKLYQR
          NYSQF..SDSDDDFVSATVPLNKKSRT..KELKQDKPK.NLNNLQKEEIP..EK.P....MALDDKLYQR
Retrocopy NYSQFGDSDSDDDFVSATVPLNKKSRTS-KELKQDKPKPNLNNLQKEEIPLEEKTPXXX>MALDDKLYQR

Parental  DLEVALALSVKELPAVTTNVQKSQDKSIEKHGNSKIETMNKSPHISNCSVASDYLDLDKITVEDDVGGVQ
          DLEVALALSVKEL..VTTNVQKSQDK..EKHGNS..ET..KSPHISNCSVASDYLDLDKIT..D..GG.Q
Retrocopy DLEVALALSVKELSTVTTNVQKSQDKRVEKHGNSRTETVGKSPHISNCSVASDYLDLDKITGKDN-GGIQ

Parental  GKRKAASKAAVQQRKILLEGSDGDSANDTEPDFAPGEDSEDDSDFCESED
          GKRKAASKAAVQQRKI.LEGSDG.SANDT.PD.A.GEDSEDDSDF.ESED
Retrocopy GKRKAASKAAVQQRKIFLEGSDGNSANDTKPDLATGEDSEDDSDFGESED

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_1595 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010098	1 retrocopy	retro_chof_2173,
Homo sapiens	ENSG00000111247	1 retrocopy	retro_hsap_2841,
Nomascus leucogenys	ENSNLEG00000003178	1 retrocopy	retro_nleu_1595 ,
Tupaia belangeri	ENSTBEG00000010089	1 retrocopy	retro_tbel_4671,