RetrogeneDB ID: retro_nleu_998

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:25525676..25526017(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MND1
• Ensembl ID: ENSNLEG00000005936
• Aliases: None
• Description: None

Sequence

>retro_nleu_998
AAAAAAGTCCTTCAAAGTTTAGTTGATAACGATATGGTTGACTGTGAGAGAACTGGAACTTCTAATTATTATCAGTCTTT
TCCAAGTAAAATTCTTCATGCAAGAACATGTAAATTGGAGGTTCTGAAATCTCAGTTGTTTCAGGCAAGCCAAAGCATGC
AAATTTACAGACAAGCATCAGAAAAACTAAAATTGGCCAACATGAGATGAAGGAGTGAACCATGCTAGCCAAAGAGCATT
CTTCACTCTGGGATCAAAGGGAACAGCTAAAGGCAGAAGTTGAAAAATGCAAATAATGTGACCCGCAAGTTGTTGAAGAA
ATACATCAGGCAAATAAAGTA

Alignment

ORF - retro_nleu_998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.04 %
• Parental protein coverage: 55.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDVLQSLVDDGMVDCERIGTSNYYWAFPSKALHAKKHKLDVLESQLSEGSQ-KHASLQKSIEKAKIGRCE
          K.VLQSLVD..MVDCER.GTSNYY..FPSK.LHA...KL.VL.SQL...SQ.KHA.LQ.SI.K.KIG..E
Retrocopy KKVLQSLVDNDMVDCERTGTSNYYQSFPSKILHARTCKLEVLKSQLFQASQ<KHANLQTSIRKTKIGQHE

Parental  TEERTRLAKELSSLRDQREQLKAEVEKYKDCDPQVVEEIRQANKV
          ..E.T.LAKE.SSL.DQREQLKAEVEK.K.CDPQVVEEI.QANKV
Retrocopy MKE*TMLAKEHSSLWDQREQLKAEVEKCK*CDPQVVEEIHQANKV

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_998 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018446	1 retrocopy	retro_amel_1745,
Callithrix jacchus	ENSCJAG00000001993	5 retrocopies	retro_cjac_1495, retro_cjac_1907, retro_cjac_2624, retro_cjac_2946, retro_cjac_3979,
Dipodomys ordii	ENSDORG00000004514	1 retrocopy	retro_dord_99,
Felis catus	ENSFCAG00000022084	1 retrocopy	retro_fcat_1833,
Macaca mulatta	ENSMMUG00000004937	1 retrocopy	retro_mmul_395,
Mus musculus	ENSMUSG00000033752	2 retrocopies	retro_mmus_1172, retro_mmus_3281,
Nomascus leucogenys	ENSNLEG00000005936	1 retrocopy	retro_nleu_998 ,
Oryctolagus cuniculus	ENSOCUG00000004594	2 retrocopies	retro_ocun_1865, retro_ocun_360,
Ochotona princeps	ENSOPRG00000015738	1 retrocopy	retro_opri_1121,
Sorex araneus	ENSSARG00000011001	1 retrocopy	retro_sara_417,