RetrogeneDB ID: retro_nleu_1840

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397312.1:9680004..9680682(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM98
• Ensembl ID: ENSNLEG00000006038
• Aliases: None
• Description: None

Sequence

>retro_nleu_1840
ATGGAGACCGTGGTGATTGTTGCCACAGGTGTGCTGGCCACCATCTTTCTGGCTTCGTTTGCAGCCTTGGTGCTGGTTTG
CAGGCAGCGCTACCACCAGCCCTGAGACCGGCGGCAGCGCTATGATTCTAAGCCCATTGTGGACCTCATCGGTGCCATGG
TGACCCGGTCTGAGCCCTCTGAGTTAGAACTGGATGATGTTGTTATCACCAACCCCCACATTGAGGCCATTCTGGAGAAC
AAAGACTGGATCGAAGACGCCTCGGGTCTCATGTCCCACTGCATTGTCATCTTGAAGATTTGTCACACTCTAACAGAGAA
GCTTGTTGCCATGACAATGGGCTCTGGGGCCAAGATGAGGACTTCAGCCATTGTCAGCGACATCGTTGTGGTGGCCAAGT
AGAACAGCCCCAGGGTAGATGATGTTGTGAAGCCGATGTACCCTCCGTTGGACCCCAAGCTCCTGGACACAGGGACGACT
GCCCTGCTCCTGTCTGTCTGTCATCTGGTGCTGGTGACAAGGAATGCCTGCCATCTGATGGGGGGCCTGGAGTGGGTTGA
CCAGTCACTATCAGCTGCTGAGGAGCATTTGGAAGTCCTTCAAGAAGCAGCCCTAGCTTTTGAGCCAGATAAAGGCCTCC
CAGGTCCCGAAGGCTTCCTGCAGGAGCAGTCTGCAATT

Alignment

ORF - retro_nleu_1840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METVVIVAIGVLATIFLASFAALVLVCRQRYCRPRDLLQRYDSKPIVDLIGAMETQSEPSELELDDVVIT
          METVVIVA.GVLATIFLASFAALVLVCRQRY..P.D..QRYDSKPIVDLIGAM.T.SEPSELELDDVVIT
Retrocopy METVVIVATGVLATIFLASFAALVLVCRQRYHQP*DRRQRYDSKPIVDLIGAMVTRSEPSELELDDVVIT

Parental  NPHIEAILENEDWIEDASGLMSHCIAILKICHTLTEKLVAMTMGSGAKMKTSASVSDIIVVAKRISPRVD
          NPHIEAILEN.DWIEDASGLMSHCI.ILKICHTLTEKLVAMTMGSGAKM.TSA.VSDI.VVAK..SPRVD
Retrocopy NPHIEAILENKDWIEDASGLMSHCIVILKICHTLTEKLVAMTMGSGAKMRTSAIVSDIVVVAK*NSPRVD

Parental  DVVKSMYPPLDPKLLDARTTALLLSVSHLVLVTRNACHLTGGLDWIDQSLSAAEEHLEVLREAALASEPD
          DVVK.MYPPLDPKLLD..TTALLLSV.HLVLVTRNACHL.GGL.W.DQSLSAAEEHLEVL.EAALA.EPD
Retrocopy DVVKPMYPPLDPKLLDTGTTALLLSVCHLVLVTRNACHLMGGLEWVDQSLSAAEEHLEVLQEAALAFEPD

Parental  KGLPGPEGFLQEQSAI
          KGLPGPEGFLQEQSAI
Retrocopy KGLPGPEGFLQEQSAI

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_1840 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014550	1 retrocopy	retro_cjac_2447,
Homo sapiens	ENSG00000006042	2 retrocopies	retro_hsap_1421, retro_hsap_3605,
Gorilla gorilla	ENSGGOG00000013333	2 retrocopies	retro_ggor_1098, retro_ggor_2432,
Myotis lucifugus	ENSMLUG00000001191	1 retrocopy	retro_mluc_130,
Macaca mulatta	ENSMMUG00000022356	2 retrocopies	retro_mmul_1835, retro_mmul_2256,
Nomascus leucogenys	ENSNLEG00000006038	3 retrocopies	retro_nleu_1233, retro_nleu_1840 , retro_nleu_2635,
Pongo abelii	ENSPPYG00000008166	2 retrocopies	retro_pabe_1175, retro_pabe_2961,
Pan troglodytes	ENSPTRG00000008993	3 retrocopies	retro_ptro_2436, retro_ptro_2990, retro_ptro_971,