RetrogeneDB ID: retro_nleu_2531

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397367.1:4843963..4844596(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5B
• Ensembl ID: ENSNLEG00000017570
• Aliases: None
• Description: None

Sequence

>retro_nleu_2531
ATGACTAGCAGAAGCACAGCTAGGCCCAATGGGCAACCCCAGGCCAGCAAAATTTGCCAGTTCAAATTGGTCCTGCTGGG
AGAATCTGCAGTGGGAAAGTCAAGCCTGGTATTACGTTTTGTCAAAGGGCAGTTCCATGAGTACCAGGAGAGCACCACTG
GAGCGGCCTTCCTCACCCAGTCCGTTTGTCTAGACGACACAACAGTCAAGTTTGAGATCTGGGACACAGCTGGGCAGGAG
CTTAGCCCCCATGTACTACAGGGCTGCCCAAGCTGCAATCGTGGTTTACAACATTACTAATCAGGAAACCTTTGCCCGAG
CAAAGACATGGGTGAAGGAACTACAGCGACAGGCCAGTCCTAGCATCGTTATTGCCCTGGCAGGGAACAAAGCTGACCTG
GCCAACAAGCGTATGGTGGAGTATGAAGAGGCCCAGGCATATGCAGATGACAACAGCTTATTGTTCATGGAGACTGCAGC
CAAAACGGCTATGAACGTGAATGATCTCTTTCTGGCAATAGCTAAGAAGTTGCCAAAGAGTGAACCCCAGAACCTGGGAG
GTGCAGCAGGCCAAAGCCAGGGTGTGGATCTCCATGAACAGTCCCACAGAACAAGAGCCAGTGTTGTAGCAAC

Alignment

ORF - retro_nleu_2531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTSRSTARPNGQPQASKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQSVCLDDTTVK
          MTSRSTARPNGQPQASKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQEST.GAAFLTQSVCLDDTTVK
Retrocopy MTSRSTARPNGQPQASKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTTGAAFLTQSVCLDDTTVK

Parental  FEIWDTAGQERYHSLAPMYYRG-AQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADLAN
          FEIWDTAGQE....L.P....G.AQAAIVVY.ITNQETFARAKTWVKELQRQASPSIVIALAGNKADLAN
Retrocopy FEIWDTAGQE----LSPHVLQG>AQAAIVVYNITNQETFARAKTWVKELQRQASPSIVIALAGNKADLAN

Parental  KRMVEYEEAQAYADDNSLLFMETSAKTAMNVNDLFLAIAKKLPKSEPQNLGGAAGRSRGVDLHEQSQ-QN
          KRMVEYEEAQAYADDNSLLFMET.AKTAMNVNDLFLAIAKKLPKSEPQNLGGAAG.S.GVDLHEQS..QN
Retrocopy KRMVEYEEAQAYADDNSLLFMETAAKTAMNVNDLFLAIAKKLPKSEPQNLGGAAGQSQGVDLHEQSH<QN

Parental  KSQCCSN
          KSQCCSN
Retrocopy KSQCCSN

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_2531 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879,
Dasypus novemcinctus	ENSDNOG00000016952	1 retrocopy	retro_dnov_350,
Equus caballus	ENSECAG00000023306	1 retrocopy	retro_ecab_280,
Echinops telfairi	ENSETEG00000009603	2 retrocopies	retro_etel_617, retro_etel_698,
Mus musculus	ENSMUSG00000000711	1 retrocopy	retro_mmus_2081,
Nomascus leucogenys	ENSNLEG00000003434	1 retrocopy	retro_nleu_2466,
Nomascus leucogenys	ENSNLEG00000017570	1 retrocopy	retro_nleu_2531 ,
Oryctolagus cuniculus	ENSOCUG00000013895	1 retrocopy	retro_ocun_1193,
Ochotona princeps	ENSOPRG00000007883	3 retrocopies	retro_opri_1061, retro_opri_1116, retro_opri_299,
Procavia capensis	ENSPCAG00000010486	1 retrocopy	retro_pcap_380,