RetrogeneDB ID: retro_nleu_1293

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397288.1:3491282..3491927(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000014655
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRKX
• Ensembl ID: ENSNLEG00000008541
• Aliases: None
• Description: None

Sequence

>retro_nleu_1293
ACTGGGACGTTCGGGCGGGTGCGCGTGGTGAAGGAGAAGACAGCCAAGCATTTCTTCGCCCTCAAGGTGATGAGCATTCC
TGATGTCATCTGCCTGAAGCAGGAGCAGCACGTGCACAATGAGAAGTCTGTCCTGAAGGAAGTCAGCCACCCGTTCCTCA
TCAGGCTGTTCTGGACGTGGCATGCCTAGCGCTTCCTCTACATGCTCATGGAGTACGTGCCGGGCGGCGAGCTCTTCAGC
TACCTGCGCAACCGGGGGCGCTTCTCCAGCACCACGGGGCTCTTCTACTCTGCAGAGATCATCTGTGCCATCGAGTACCT
GCACTACAAAGAGATTGTCTACAGGGACTTGAAGCCAGAGAACATCCTGCTGGATAGGGATGGCCACATCAAGCTCACGG
ACTTTGGGTTCGCCAAGAAGCTGGTAGACAGGACTTGGACCGTCTGCGGAACACCTGAGTACCTGGCCCCCGAAGTCATT
CAGAGCAAGGGCCACGGAAGGGCCGTGGACTGGTGGGCCCTCGGCATCCTGATATTCGAGATGCTCTCAGGATTTCCCCC
GTTTTTTGATGATAACCCGTTTGGCATTTATCAGATTCTTGCAGGCAAAATAGATTTCCCCAGACATTTGGATTTCCATG
TAAAA

Alignment

ORF - retro_nleu_1293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.3 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TGTFGRVHLVKEKTAKHFFALKVMSIPDVIRLKQEQHVHNEKSVLKEVSHPFLIRLFWTWHDERFLYMLM
          TGTFGRV..VKEKTAKHFFALKVMSIPDVI.LKQEQHVHNEKSVLKEVSHPFLIRLFWTWH..RFLYMLM
Retrocopy TGTFGRVRVVKEKTAKHFFALKVMSIPDVICLKQEQHVHNEKSVLKEVSHPFLIRLFWTWHA*RFLYMLM

Parental  EYVPGGELFSYLRNRGRFSSTTGLFYSAEIICAIEYLHSKEIVYRDLKPENILLDRDGHIKLTDFGFAKK
          EYVPGGELFSYLRNRGRFSSTTGLFYSAEIICAIEYLH.KEIVYRDLKPENILLDRDGHIKLTDFGFAKK
Retrocopy EYVPGGELFSYLRNRGRFSSTTGLFYSAEIICAIEYLHYKEIVYRDLKPENILLDRDGHIKLTDFGFAKK

Parental  LVDRTWTLCGTPEYLAPEVIQSKGHGRAVDWWALGILIFEMLSGFPPFFDDNPFGIYQKILAGKIDFPRH
          LVDRTWT.CGTPEYLAPEVIQSKGHGRAVDWWALGILIFEMLSGFPPFFDDNPFGIYQ.ILAGKIDFPRH
Retrocopy LVDRTWTVCGTPEYLAPEVIQSKGHGRAVDWWALGILIFEMLSGFPPFFDDNPFGIYQ-ILAGKIDFPRH

Parental  LDFHVK
          LDFHVK
Retrocopy LDFHVK

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_1293 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000000005	1 retrocopy	retro_mdom_1224,
Nomascus leucogenys	ENSNLEG00000008541	1 retrocopy	retro_nleu_1293 ,
Nomascus leucogenys	ENSNLEG00000009888	1 retrocopy	retro_nleu_2469,
Drosophila melanogaster	FBgn0000489	1 retrocopy	retro_dmel_60,