RetrogeneDB ID: retro_nleu_1826

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397312.1:8926914..8927379(+)
• Located in intron of: ENSNLEG00000013033

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCGF3
• Ensembl ID: ENSNLEG00000000926
• Aliases: None
• Description: None

Sequence

>retro_nleu_1826
ATGTTGACCAGAAGGATTAAGCTATGGGACACTAAGGCCCACATCACCTGCCGCCTGTGTAGTGGGCACCTCATTGATGC
AACCATGGTGACCAAGTGTCTGCATACATTCTGTAGGGGTTGCCTGGGAAAGTATTTGTAAGAGAACAACACCTGCCCTG
CATGTAGGACTGTGATGCGTCACACCCACTCACTGCAGTACATCAGTCATGACAGCACCATACATGATACTGTTTACAAA
CTGGTATCAGCACTCCAAGAAGCAGAAATGAAAACAAGAGAATTCTGTCACAAATTGGGCATGGAAGTGTCTGGAGACAT
CAAGGGGGAGACTTGTTCCACAAAACAACACTTAGATTTCCATCAGAATGGTGAAACGAAAGCAGAAGACAGTTCAAACA
AAGAGACCAAAAAAGAGAAGAAGGAAAAGGACAACGATTTTCACAGAAGCGATGAGCAGGAAAGC

Alignment

ORF - retro_nleu_1826 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.64 %
• Parental protein coverage: 64.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLTRKIKLWDINAHITCRLCSGYLIDATTVTECLHTFCRSCLVKYLEENNTCPTCRIVIHQSHPLQYIGH
          MLTR.IKLWD..AHITCRLCSG.LIDAT.VT.CLHTFCR.CL.KYL.ENNTCP.CR.V....H.LQYI.H
Retrocopy MLTRRIKLWDTKAHITCRLCSGHLIDATMVTKCLHTFCRGCLGKYL*ENNTCPACRTVMRHTHSLQYISH

Parental  DRTMQDIVYKLVPGLQEAEMRKQREFYHKLGMEVPGDIKGETCSAKQHLDSHRNGETKADDSSNKEAAEE
          D.T..D.VYKLV..LQEAEM.K.REF.HKLGMEV.GDIKGETCS.KQHLD.H.NGETKA.DSSNKE...E
Retrocopy DSTIHDTVYKLVSALQEAEM-KTREFCHKLGMEVSGDIKGETCSTKQHLDFHQNGETKAEDSSNKETKKE

Parental  KPEEDNDYHRSDEQVS
          K.E.DND.HRSDEQ.S
Retrocopy KKEKDNDFHRSDEQES

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_1826 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001960	1 retrocopy	retro_cjac_707,
Macaca mulatta	ENSMMUG00000012624	1 retrocopy	retro_mmul_2182,
Monodelphis domestica	ENSMODG00000005677	3 retrocopies	retro_mdom_1481, retro_mdom_885, retro_mdom_985,
Nomascus leucogenys	ENSNLEG00000000752	1 retrocopy	retro_nleu_907,
Nomascus leucogenys	ENSNLEG00000000926	1 retrocopy	retro_nleu_1826 ,
Otolemur garnettii	ENSOGAG00000015569	1 retrocopy	retro_ogar_2846,