RetrogeneDB ID: retro_nleu_1420

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397292.1:11900475..11901562(-)
• Located in intron of: ENSNLEG00000003723

Retrocopy information

• Ensembl ID: ENSNLEG00000003724
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GCAT
• Ensembl ID: ENSNLEG00000014866
• Aliases: None
• Description: None

Sequence

>retro_nleu_1420
ATCCGCGTGAACGGCGTCTCCGGAGGAATCCTTAACTTCTGTGCCAACAATTACCTGGGACTGAGCAGCCACCCTGAGGT
GATCCAGGCAGGTCTGCAGGCTCTGGAGGAGTTTGGAGCTGGCCTCAGCTCTGTCCGCTTTATCTGTGGAACCCAGAGCA
TCCACAAGGATGTAGAAGCAAAAATAGCCCGCTTCCACCAGCGGGAGGATGCCATCTTCTATCCCAGCTGTTTTGACGCC
AAGGCCGGCCTCTTTGAGGCCCCGCTGACCCTGGAGGACGCAGTCCTGTCGGACGAGCTGAACCATGCCTCCATCATCGA
CGGCATCCGCCTGTGCAAGGCCCACAAGTACTGCTATCGCCACCTGGACATGGCCGACCTAGAAGCCAAGCTGCAGGAGG
CCCAGAAGCATCGGCTGCACCTGGTGGCCACTGACGGGGCCTTTTCCATGGATGGCGACATCGCACGCCTGCAGGAGATC
TGCCGCCTCGCCTCTAGATATGGCGCCCTGGTCTTTGCGGATGAATGCCATGCCACTGGCTTCCTGGGGCCCACAGGACG
GGGCACAGATGAGCCGCTGGGTGTGATTGACCAGGTCACCATCATCAACTCCACCCTGGGGAAGGCTCTGGGTAGAGCAT
CGGGGGGGCTACACGACAGGGCCTCGGCCCCTGGTGTCCTTGCTGCGGCAGCGCGCCCGGCCCTACCTCTTCTCCAATAG
TCTGCCACCTGCTGTTGTTGGCTACGCCTCCAAGGCCCTAGATCTGCTCATGGAGAGTAACACCATTGTCCAGTCTATGG
CTGCCAAGATCCAGAGGTTCCGTAGTAAGATGGAAGCTGCTGGCTTCACTATCTCGGGAGCCAGTCACCCAATCTGCCCT
GTGATCCTGGGTGATGCCCGGCTGGCCTCTCACATGGCGGATGACATGCTGGAGAGAGGCATCTTTGTCATCGGGTTCAG
CTACCCCGTGGTCCCCGAGGGCAAGGCCCGGATCCGGGTACAGATCTCAGCAGTGCACAGCGAGGAAGACATTGACCGCT
GCGTGGAGGCCTTCGTGCAAGTGGGGCGACTGCATGGGGCACTGCCC

Alignment

ORF - retro_nleu_1420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 81.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IHLLSFTSGILNFCANNYLGLSSHPEVIQAGLQALEEFGAGLSSVRFICGTQSIHKNLEAKIARFHQRED
          I.......GILNFCANNYLGLSSHPEVIQAGLQALEEFGAGLSSVRFICGTQSIHK..EAKIARFHQRED
Retrocopy IRVNGVSGGILNFCANNYLGLSSHPEVIQAGLQALEEFGAGLSSVRFICGTQSIHKDVEAKIARFHQRED

Parental  AILYPSCFDANAGLFEALLTPEDAVLSDELNHASIIDGIRLCEAHKYLXXXXXXXXXHLLMSFLQKHRLR
          AI.YPSCFDA.AGLFEA.LT.EDAVLSDELNHASIIDGIRLC.AHKY.................QKHRL.
Retrocopy AIFYPSCFDAKAGLFEAPLTLEDAVLSDELNHASIIDGIRLCKAHKYCYRHLDMADLEAKLQEAQKHRLH

Parental  LVATDGAFSMDGDIAPLQEICRLASRYGALVFVDECHATGFLGPTGRGTDELLGVMDQVTIINSTLGKAL
          LVATDGAFSMDGDIA.LQEICRLASRYGALVF.DECHATGFLGPTGRGTDE.LGV.DQVTIINSTLGKAL
Retrocopy LVATDGAFSMDGDIARLQEICRLASRYGALVFADECHATGFLGPTGRGTDEPLGVIDQVTIINSTLGKAL

Parental  GGASGG-YTTGPGPLVSLLRQRARPYLFSNSLPPAVVGCASKALDLLMESNTVVQSMAAKTQRFRSKMEA
          G.ASGG.YTTGP.PLVSLLRQRARPYLFSNSLPPAVVG.ASKALDLLMESNT.VQSMAAK.QRFRSKMEA
Retrocopy GRASGG>YTTGPRPLVSLLRQRARPYLFSNSLPPAVVGYASKALDLLMESNTIVQSMAAKIQRFRSKMEA

Parental  AGFTISGASHPICPVMLGDARLASRMADDMLKRGIFVIGFSYPVSPRARPG-SVQISAVHSEEDIDRCVG
          AGFTISGASHPICPV.LGDARLAS.MADDML.RGIFVIGFSYPV.P.......VQISAVHSEEDIDRCV.
Retrocopy AGFTISGASHPICPVILGDARLASHMADDMLERGIFVIGFSYPVVPEGKARIRVQISAVHSEEDIDRCVE

Parental  AFVEVGRLHGALP
          AFV.VGRLHGALP
Retrocopy AFVQVGRLHGALP

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_1420 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000003987	1 retrocopy	retro_ggor_1102,
Nomascus leucogenys	ENSNLEG00000014866	1 retrocopy	retro_nleu_1420 ,