RetrogeneDB ID: retro_nleu_1191

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397284.1:26801865..26802626(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTOV1
• Ensembl ID: ENSNLEG00000005374
• Aliases: None
• Description: None

Sequence

>retro_nleu_1191
CAACTGGCACAGTTCCACTTCACCAACAGAGACTGCGGCTGCTCAGTGGGCTCTGCCACGTCATGGGCAATGGCTTCGCG
GGCTGCATGCTGTTTCCCCACATCTCCCCCTGCGAGATGTGCGTGCTCATGCTCCTGTACTCTTCCAAGAGGAAGATCTT
CATGGGCTTCATCCCCTACGACCAGAGCGGCTTAGTCAGCGCCATCCGGCAGGTCATCACTACCCGCAAGCAAGCAGTGG
GACCTGGTGGTGTCAACTCAGGCCCAGTCCAGATCGTCAACAAGTTCCTGGCGTGGAGCGGCATCGTGGAGTGGCAGGAA
CCCAGGCCTGAGCCCAACAGTCAGTCCAAGAGGTGGCTGCCGTCCCACGTCTAGGTGAACCAGGGGGAGATCCTGAGGAC
CGAGCAGTGGACGAGGAAGCTGTACATGCAGCTCATCCCGCAGCAGCTGCTGACCACCCTGTGCTGCTGTTGCGGAACTT
GCCCCTGGTGCAGTTCCACTTCACCAAGGACTTGGAGACGCTGAAGAGCCTGTGCCAGATCATGGACAATGGCTTCACCG
GCTGAGTGCATTTTTCCTACAAAGCGTTGTGTGAGATCCGCGTGCTCATGCTCCTGTACTCTGAGAAGAAAATCTTCATC
GGCCTCATCCCCCGTGACCCAGGGCAACTTCCTCAACGGCATATGGCGAGTCGTTGCCAACCAGCAGCAGGTCCTGCAGT
GGAACCTGGAGCAGGAGCAGCAGCAGCAAGGAATGGAGGGT

Alignment

ORF - retro_nleu_1191 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.49 %
• Parental protein coverage: 54.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QLAQFHFTNRDCDS-LKGLCRIMGNGFAGCMLFPHISPCEVRVLMLLYSSKKKIFMGLIPYDQSGFVSAI
          QLAQFHFTNRDC...L.GLC..MGNGFAGCMLFPHISPCE..VLMLLYSSK.KIFMG.IPYDQSG.VSAI
Retrocopy QLAQFHFTNRDCGC<LSGLCHVMGNGFAGCMLFPHISPCEMCVLMLLYSSKRKIFMGFIPYDQSGLVSAI

Parental  RQVITTRKQAVGPGGVNSGPVQIVNNKFLAWSGVMEWQEPRPEPNSRSKRWLPSHVYVNQGEILRTEQWP
          RQVITTRKQAVGPGGVNSGPVQIVN.KFLAWSG..EWQEPRPEPNS.SKRWLPSHV.VNQGEILRTEQW.
Retrocopy RQVITTRKQAVGPGGVNSGPVQIVN-KFLAWSGIVEWQEPRPEPNSQSKRWLPSHV*VNQGEILRTEQWT

Parental  RKLYMQLIPQQLLTTL-VPLFRNSRLVQFHFTKDLETLKSLCRIMDNGFAGCVHFSYKASCEIRVLMLLY
          RKLYMQLIPQQLLTTL.V.L.RN..LVQFHFTKDLETLKSLC.IMDNGF.G.VHFSYKA.CEIRVLMLLY
Retrocopy RKLYMQLIPQQLLTTL<VLLLRNLPLVQFHFTKDLETLKSLCQIMDNGFTG*VHFSYKALCEIRVLMLLY

Parental  SSEKKIFIGLIPHD-QGNFVNGIRRVIANQQQVLQRNLEQEQQQRGMGG
          .SEKKIFIGLIP.D.QGNF.NGI.RV.ANQQQVLQ.NLEQEQQQ.GM.G
Retrocopy -SEKKIFIGLIPRD>QGNFLNGIWRVVANQQQVLQWNLEQEQQQQGMEG

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_1191 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003495	1 retrocopy	retro_cfam_289,
Callithrix jacchus	ENSCJAG00000004105	1 retrocopy	retro_cjac_445,
Homo sapiens	ENSG00000104960	1 retrocopy	retro_hsap_2694,
Gorilla gorilla	ENSGGOG00000010182	1 retrocopy	retro_ggor_1877,
Macaca mulatta	ENSMMUG00000011618	1 retrocopy	retro_mmul_1426,
Nomascus leucogenys	ENSNLEG00000005374	1 retrocopy	retro_nleu_1191 ,
Pongo abelii	ENSPPYG00000010265	1 retrocopy	retro_pabe_2288,
Pan troglodytes	ENSPTRG00000011321	1 retrocopy	retro_ptro_1818,