RetrogeneDB ID: retro_nleu_900

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:4084220..4084888(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC6
• Ensembl ID: ENSNLEG00000012518
• Aliases: None
• Description: None

Sequence

>retro_nleu_900
CTCTTACAAACACATTTATTTCAGTGGGTAGGAATAATGCCTCCAAAATGCTGTTTGTTACACGGACCACCAGGTATGGG
AAAAACACTCTTGGCACGAGCTGTTGCTAGCCAGTTGGACTACAGTTTCTTAAAGGTTGTATCTAGTTCTATTGTAGACA
AGTACATTGGTGAAAGTGCTTGTTTGATCAGAGAAATGTTTAATTATCCCAGGGACCATCAACCATGCATCATTTTTATG
GATGAAATAGATGCTATTGGTGGTTGTCCGTTTTCTGAGAGTACTTCAGCTGACAGAGAGATTCAGAGTACTTTAATGGA
GTTACTGAATCAAATGGATGGATTTGATACTCTGCACAGAGTTAAGATGATCATGACTACAAACGACCAGATACACTGGA
TCCTGCTTTGCTGTATCCGGGAAGATTAGATAGAAAAATACATATCGATTTGCCATATGAACAAGCAAGATTAGACCTAC
TGAAAATCCATGCAGGTCCCATTACAAAGCGTGGTGAGAGAGATTAGGAAGCAATTGTGAAGCTTTCAGATGGCTTTAAT
GGAGTAGACCTGAGAAATGTTTGTACTGCAGCAGGCATGTTCGCAATTCGTGCTGATCATGATTTTGTAGTACAGGAAGA
CTTCATGAAAGCAGTCAGAAAAGTGGCT

Alignment

ORF - retro_nleu_900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.95 %
• Parental protein coverage: 55.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTNPELFQRVGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNYA
          L....LFQ.VGI.PPK.CLL.GPPG.GKTLLARAVASQLD..FLKVVSSSIVDKYIGESA.LIREMFNY.
Retrocopy LLQTHLFQWVGIMPPKCCLLHGPPGMGKTLLARAVASQLDYSFLKVVSSSIVDKYIGESACLIREMFNYP

Parental  RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATN-RPDTLDPALLR
          RDHQPCIIFMDEIDAIGG..FSE.TSADREIQ.TLMELLNQMDGFDTLHRVKMIM.TN.RPDTLDPALL.
Retrocopy RDHQPCIIFMDEIDAIGGCPFSESTSADREIQSTLMELLNQMDGFDTLHRVKMIMTTN<RPDTLDPALLY

Parental  PGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVCTEAGMFAIRADHDF
          PGRLDRKIHIDLP.EQARLD.LKIHAGPITK.GE.D.EAIVKLSDGFNG.DLRNVCT.AGMFAIRADHDF
Retrocopy PGRLDRKIHIDLPYEQARLDLLKIHAGPITKRGERD*EAIVKLSDGFNGVDLRNVCTAAGMFAIRADHDF

Parental  VVQEDFMKAVRKVA
          VVQEDFMKAVRKVA
Retrocopy VVQEDFMKAVRKVA

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_900 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007126	2 retrocopies	retro_cjac_204, retro_cjac_3221,
Cavia porcellus	ENSCPOG00000009477	1 retrocopy	retro_cpor_47,
Homo sapiens	ENSG00000100519	2 retrocopies	retro_hsap_1022, retro_hsap_4059,
Gorilla gorilla	ENSGGOG00000002152	2 retrocopies	retro_ggor_2727, retro_ggor_808,
Macropus eugenii	ENSMEUG00000007084	3 retrocopies	retro_meug_1700, retro_meug_2090, retro_meug_923,
Monodelphis domestica	ENSMODG00000014500	1 retrocopy	retro_mdom_438,
Nomascus leucogenys	ENSNLEG00000012518	2 retrocopies	retro_nleu_559, retro_nleu_900 ,
Otolemur garnettii	ENSOGAG00000010011	1 retrocopy	retro_ogar_3101,
Pongo abelii	ENSPPYG00000005820	2 retrocopies	retro_pabe_3334, retro_pabe_858,
Pan troglodytes	ENSPTRG00000006352	2 retrocopies	retro_ptro_2752, retro_ptro_699,
Rattus norvegicus	ENSRNOG00000007203	1 retrocopy	retro_rnor_1480,
Tursiops truncatus	ENSTTRG00000003880	1 retrocopy	retro_ttru_117,