RetrogeneDB ID: retro_nleu_1481

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397296.1:1267281..1267885(+)
• Located in intron of: ENSNLEG00000018003

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2A
• Ensembl ID: ENSNLEG00000014794
• Aliases: None
• Description: None

Sequence

>retro_nleu_1481
AAGAGACGAAGTAGCTCATATATACCAGAATACTGACAGCGAAGGAGCCGAAGTCATTCTCCAATGTCTAACCGGAGAAG
ACATACTGGCAGAAGGGCAAATCCAGATCCCAACACTTGCCTTAGAGTGTTTGGCCTTAGTTTGTACACAACAGACAGAG
ATCTTCGTGAAGTATGTTCTCGATATGGAACTTTGAATGGTGCCAATGTGGTTTACAATCAGCAAACTGGGCGATCTCAA
GGATTTGCTTTTGTGTATTTTGAGGGAATAGATGACTCAAAGGAGGCTATGGTAAGGGCAAATAGAAAGGAGCTGGATGA
CAGAAGAAATTCGGGTGGATTTTTCTATTACCAAGAGAATGCACACACCTACACCAGGCATCTATATGGGCAGAACAACT
CATAGTGGTGGTGGCAGAGGTGGTGGTAAAGGCGGCAGTGGAGGTGGTCACAGACGTCGAGATTCTTACTATGATAGAGG
ATATGATCGTGGATATGACAGATATGAAGACTATGATTACCAGTACAGAAGATGATCACTTTCTCCTTATTATAGTCGAT
ACAGATCACAATCAAGATCTCATTCCTACAGCCCAAGACACTAT

Alignment

ORF - retro_nleu_1481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.27 %
• Parental protein coverage: 71.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSRSRSYTPEYRRRRSRSHSPMSNRRRHTGSRANPDPNTCLGVFGLSLYTTERDLREVFSRYGPLSGVNV
          ..RS.SY.PEY..RRSRSHSPMSNRRRHTG.RANPDPNTCL.VFGLSLYTT.RDLREV.SRYG.L.G.NV
Retrocopy KRRSSSYIPEY*QRRSRSHSPMSNRRRHTGRRANPDPNTCLRVFGLSLYTTDRDLREVCSRYGTLNGANV

Parental  VYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRR-IRVDYSITKRAHTPTPGIYMGRPTHSGGGG
          VY.Q.TGRS.GFAFVYFE.IDDSKEAM.RAN..ELD.RR.IRVD.SITKR.HTPTPGIYMGR.THS.GGG
Retrocopy VYNQQTGRSQGFAFVYFEGIDDSKEAMVRANRKELDDRR>IRVDFSITKRMHTPTPGIYMGRTTHS-GGG

Parental  GGGGGGGGGGGGRRRDSYYDRGYDRGYDRYEDYDYRYRRRSPSPYYSRYRSRSRSRSYSPRRY
          .GGG.GG.GGG.RRRDSYYDRGYDRGYDRYEDYDY.YRR.S.SPYYSRYRS.SRS.SYSPR.Y
Retrocopy RGGGKGGSGGGHRRRDSYYDRGYDRGYDRYEDYDYQYRR*SLSPYYSRYRSQSRSHSYSPRHY

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_1481 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001130	1 retrocopy	retro_chof_974,
Callithrix jacchus	ENSCJAG00000001509	1 retrocopy	retro_cjac_1759,
Echinops telfairi	ENSETEG00000007250	2 retrocopies	retro_etel_323, retro_etel_692,
Homo sapiens	ENSG00000164548	1 retrocopy	retro_hsap_386,
Gorilla gorilla	ENSGGOG00000009053	1 retrocopy	retro_ggor_391,
Mustela putorius furo	ENSMPUG00000013480	1 retrocopy	retro_mputfur_1442,
Nomascus leucogenys	ENSNLEG00000007841	2 retrocopies	retro_nleu_2591, retro_nleu_867,
Nomascus leucogenys	ENSNLEG00000014794	1 retrocopy	retro_nleu_1481 ,
Otolemur garnettii	ENSOGAG00000009733	3 retrocopies	retro_ogar_1966, retro_ogar_2558, retro_ogar_3027,
Pongo abelii	ENSPPYG00000017728	1 retrocopy	retro_pabe_324,
Pan troglodytes	ENSPTRG00000018988	1 retrocopy	retro_ptro_299,
Sorex araneus	ENSSARG00000012900	1 retrocopy	retro_sara_467,