RetrogeneDB ID: retro_nleu_1009

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:11034028..11034631(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIT2
• Ensembl ID: ENSNLEG00000002631
• Aliases: None
• Description: nitrilase family, member 2 [Source:HGNC Symbol;Acc:29878]

Sequence

>retro_nleu_1009
TTCCACTTGGCCCTCATCCAGCTTCAAGTTTCTTCATCAAATCAGATAACAACACTTGAGCTTGTAGCCTTGTCCGGGAG
ACAGCAACACAAGGAGCAAAATAGTTTGTTTGTTGGAATGCTTTAATTCTCCCTATGGCACAAAATATTTTCCTGAATAT
GCAGCGAAAATTCCTGGTAAATCCACACAGAAGCTTTCTGAAGTAGCAAAGGAATACAGCCTCACTAGAGGGTCCATCCC
TGAAAAGGATGCTGGGAAATTAGATAACACCTGTGCTGTGTTTGTACCTCATGGAACTTTACTAGTAAAGCAAAGAAAGG
TCCATCTGCTTGACACTGGTGTTCCTAGAAAAATGACGTTTCAAGAATCCACAATGTTGAATCCCGGCAATAGTTTCTCC
ACATTTGATACTCCGTACTGCAGAATGAGTCGGGGCATCTGCTATGACGTTGGTTTGCAGAGCTTGCACAAATCTACACA
CGGAGAGGCTGCCAGCTGTTGGTTTATCCAGGGGATTTCAGTTTGACCACTGGACCAGCCCACTGGGAATTGCTTCAGGC
TCTTGATAATCAGGTGTATGTGGCCACACTCTCCTGCCCGAGA

Alignment

ORF - retro_nleu_1009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.76 %
• Parental protein coverage: 72.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FRLALIQLQISS-IKSDNVIRACSFIREAATQGAK-IISLPECFNSPYGTKYFPEYAEKIPGESTQKLSE
          F.LALIQLQ.SS.IKSDN...ACS..RE.ATQGAK.I..L.ECFNSPYGTKYFPEYA.KIPG.STQKLSE
Retrocopy FHLALIQLQVSS<IKSDNNT*ACSLVRETATQGAK<IVCLLECFNSPYGTKYFPEYAAKIPGKSTQKLSE

Parental  VAKECSIYLIGGSIPEEDAGKLYNTCAVFGPDGTLLAKYRKIHLFDIDVPGKITFQESKTLSPGDSFSTF
          VAKE.S..L..GSIPE.DAGKL.NTCAVF.P.GTLL.K.RK.HL.D..VP.K.TFQES..L.PG.SFSTF
Retrocopy VAKEYS--LTRGSIPEKDAGKLDNTCAVFVPHGTLLVKQRKVHLLDTGVPRKMTFQESTMLNPGNSFSTF

Parental  DTPYCRVGLGICYDMR-FAELAQIYAQRGCQLLVYPGAFNLTTGPAHWELLQRSRAVDNQVYVATASPAR
          DTPYCR...GICYD...FAELAQIY..RGCQLLVYPG.F.LTTGPAHWELLQ...A.DNQVYVAT.S..R
Retrocopy DTPYCRMSRGICYDVG<FAELAQIYTRRGCQLLVYPGDFSLTTGPAHWELLQ---ALDNQVYVATLSCPR

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_1009 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003980	1 retrocopy	retro_amel_1002,
Callithrix jacchus	ENSCJAG00000000590	1 retrocopy	retro_cjac_3014,
Homo sapiens	ENSG00000114021	1 retrocopy	retro_hsap_411,
Gorilla gorilla	ENSGGOG00000003724	1 retrocopy	retro_ggor_406,
Macaca mulatta	ENSMMUG00000020024	2 retrocopies	retro_mmul_1758, retro_mmul_505,
Mustela putorius furo	ENSMPUG00000011450	1 retrocopy	retro_mputfur_805,
Nomascus leucogenys	ENSNLEG00000002631	1 retrocopy	retro_nleu_1009 ,
Pan troglodytes	ENSPTRG00000015161	1 retrocopy	retro_ptro_315,