RetrogeneDB ID: retro_nleu_1905

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397315.1:2655463..2656038(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12ORF29
• Ensembl ID: ENSNLEG00000005396
• Aliases: None
• Description: None

Sequence

>retro_nleu_1905
GATCAGCCATAGCTTTCGGCTCGACTAGACAGAAAGCCCAACAAACAAGTTGAAAAAAGATTTTAACATTTTCTACATTC
AAATGAAAACCCAAAATAATTTTTTTTTGAAACGTTGAGGAGGACTTCAAACCGGTTCTAGAGTGCTGGATACCAGCAAA
GGAAATAGAACAAATAAATGGGAACCCAGTGCCTAATGAAAATAGATACATTCCTGATTGGGTACCAGTATAGAAAAATA
ACAAACAGTATTGCTGGCATTCCTCTGTAGTTAGTTATGAATTTGAAATTGCCCTGGTACTAAAACATCATGCTGATGAT
TCTGAACTTCTGGAAATTACTGCAGTGCCACTATCAGATTTCTTAGAACAAACACTGGAGCTCACAGGAAAAAATATCAA
TGGAAACCCATATGGGTTAGGGAGCAAGAAACATCCATTACATCTTCTTATACCACATGGAGCATTTCAAATAAGAAATC
TACCTTCGTTGAAGCACAATGATCTCTTGTCCTCGTTTGAAGGTTGCAAAGTGGGTAAAATTGAAGAAATAGTATGGCAT
CGCAGTGATGGCTGT

Alignment

ORF - retro_nleu_1905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.94 %
• Parental protein coverage: 58.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DQPYLWARLDRKPNKQAEKRFKNFLHSKEN-PK-EFFWNVEEDFKLAPECWIPAKEIEQINGNPVPDENG
          DQP.L.ARLDRKPNKQ.EKRF..FLHS.EN.PK.....NVEEDFK...ECWIPAKEIEQINGNPVP.EN.
Retrocopy DQP*LSARLDRKPNKQVEKRF*HFLHSNEN<PKIXXXXNVEEDFKPVLECWIPAKEIEQINGNPVPNENR

Parental  HIPGWVPVEKNNKQYCWHSSVVNYEFEIALVLKHHPDDSGLLEISAVPLSDLLEQTLELIGTNINGNPYG
          .IP.WVPV.KNNKQYCWHSSVV.YEFEIALVLKHH.DDS.LLEI.AVPLSD.LEQTLEL.G.NINGNPYG
Retrocopy YIPDWVPV*KNNKQYCWHSSVVSYEFEIALVLKHHADDSELLEITAVPLSDFLEQTLELTGKNINGNPYG

Parental  LGSKKHPLHLLIPHGAFQIRNLPSLKHNDLLSWFEGCKEGKIEGIVWHCSDGC
          LGSKKHPLHLLIPHGAFQIRNLPSLKHNDLLS.FEGCK.GKIE.IVWH.SDGC
Retrocopy LGSKKHPLHLLIPHGAFQIRNLPSLKHNDLLSSFEGCKVGKIEEIVWHRSDGC

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_1905 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011011	1 retrocopy	retro_chof_1262,
Homo sapiens	ENSG00000133641	1 retrocopy	retro_hsap_3984,
Gorilla gorilla	ENSGGOG00000005986	1 retrocopy	retro_ggor_2674,
Loxodonta africana	ENSLAFG00000013286	1 retrocopy	retro_lafr_706,
Macaca mulatta	ENSMMUG00000015860	1 retrocopy	retro_mmul_715,
Nomascus leucogenys	ENSNLEG00000005396	1 retrocopy	retro_nleu_1905 ,
Pan troglodytes	ENSPTRG00000005277	1 retrocopy	retro_ptro_2704,
Rattus norvegicus	ENSRNOG00000006973	1 retrocopy	retro_rnor_1625,
Tupaia belangeri	ENSTBEG00000005256	1 retrocopy	retro_tbel_94,
Tarsius syrichta	ENSTSYG00000014665	1 retrocopy	retro_tsyr_1572,