RetrogeneDB ID: retro_nleu_2199

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397333.1:11758432..11758915(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NICN1
• Ensembl ID: ENSNLEG00000006851
• Aliases: None
• Description: None

Sequence

>retro_nleu_2199
TACTAAACAGCTTTTTTGAGCATCCATGTCTGTCAGCACACCTCAGCACACACACCGGCCAAGTGGGTGACCTACCTGCG
GGACTACTGTCTGATGCCCTACCCACACAGTGAGGAGGGAGCCCAGGAGTATGTGTCGCTGTTCAAGCATCAGATACTGT
GTGACACGGCCAGAGTATCGGAGCTACACCTGATTCTGCGGCAGCCATCACCATTGTGGCTGTCTTTCACAGTGGAGGAG
CTGCAGATCTATCAGCAAGGACCAAAAAGCCCCTCCATGATCTTCCCCAAGTGGCTCTCCCACCCAGTGCCCTGTGAGCA
ACCTGCACTCCTCCATGAGGGTCTGCCAGACCCCAGCAGGATATCCTCTGAGGTGCAGCAGATGTGGGCACTGACAGAGA
TGATCCGGGCCAGTCACACCTCCGCAAGGATCGGCCACTTTGATGTAGATGGCTGTTATGACCTGAACTTGCTCTCCTAC
ACT

Alignment

ORF - retro_nleu_2199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.68 %
• Parental protein coverage: 75.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YYTAFLSIRVRQHTSAHTPAKWVTCLRDYCLMPDPHSEEGAQEYVSLFKHQMLCDMARISELRLILRQPS
          Y.TAFLSI.V.QHTSAHTPAKWVT.LRDYCLMP.PHSEEGAQEYVSLFKHQ.LCD.AR.SEL.LILRQPS
Retrocopy Y*TAFLSIHVCQHTSAHTPAKWVTYLRDYCLMPYPHSEEGAQEYVSLFKHQILCDTARVSELHLILRQPS

Parental  PLWLSFTVEELQIYQQGPKSPSVTFPKWLSHPVPCEQPALLREGLPDPSRVSSEVQQMWALTEMIRASHT
          PLWLSFTVEELQIYQQGPKSPS..FPKWLSHPVPCEQPALL.EGLPDPSR.SSEVQQMWALTEMIRASHT
Retrocopy PLWLSFTVEELQIYQQGPKSPSMIFPKWLSHPVPCEQPALLHEGLPDPSRISSEVQQMWALTEMIRASHT

Parental  STRIGRFDVDGCYDLNLLSYT
          S.RIG.FDVDGCYDLNLLSYT
Retrocopy SARIGHFDVDGCYDLNLLSYT

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_2199 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
Homo sapiens	ENSG00000145029	1 retrocopy	retro_hsap_4824,
Nomascus leucogenys	ENSNLEG00000006851	1 retrocopy	retro_nleu_2199 ,
Pongo abelii	ENSPPYG00000029914	1 retrocopy	retro_pabe_3751,
Pan troglodytes	ENSPTRG00000032494	1 retrocopy	retro_ptro_3211,