RetrogeneDB ID: retro_nleu_1513

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397297.1:19636151..19636728(+)
• Located in intron of: ENSNLEG00000015289

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM54A
• Ensembl ID: ENSNLEG00000014793
• Aliases: None
• Description: None

Sequence

>retro_nleu_1513
GAATATTCTGGCGTTCCTATAGATCAGGTTTTGCTGATTTGGGAAAATAAAGACTATGGATCAACTAGGAATACTGTTCA
TATTAATGAGAAAATACTTCTGTTAGAACCTTGTTGAAGGCACAATTTTGAGTTGATCCAGTTCTTGAACTCTATAGACT
CTGATAATTCTGGATCTATTGTTCCATCTTTTGCTGATATTTTGTGTGTGGCAAATGTCGAGGAAGCCAGTTTTCTCAGA
TTTCAAAATAGTATATGGAAAAATGAAGAGAAAATGGAATGTGTCCATCCTTTGCAACTAGTTTGGGATCCACTGTCATC
TGCTCTGAAACACAACAAACCAGTGAAAAATGATCTTGTAAATGAAGCTGCAATTAAAAAAAATAGGTGCCCCTGAAGTT
GAGCTAACTTTTCTTCACTCTCAGATTCCTGCAATTGTGGAAATGCAGGAACTGAAAAACAGTACAAATTCTAGTTCCTT
TGGCTTGAATGATGGGCCCATTAGTTTGGGACAAATGCCATCATCAGGGGCTGTTCAGCTGAGTGGGGAGTCACACATAT
ATATTTGTTCTTTACTG

Alignment

ORF - retro_nleu_1513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 50.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EYFGVPVEQVLLIWENKDYGSTRSIVRIIGKMLPLEPCRRPNFELIPLLNSVDSGNRGSMVPSFADILYV
          EY.GVP..QVLLIWENKDYGSTR..V.I..K.L.LEPC.R.NFELI..LNS.DS.N.GS.VPSFADIL.V
Retrocopy EYSGVPIDQVLLIWENKDYGSTRNTVHINEKILLLEPC*RHNFELIQFLNSIDSDNSGSIVPSFADILCV

Parental  ANDEEVSYLRFRNSIWKNEEEKVEIFQPLRLVRDPLSPAVRQNETVKNDLPVNEAAI-KKIAALENELTF
          AN.EE.S.LRF.NSIWKN.EEK.E...PL.LV.DPLS.A...N..VKNDL.VNEAAI.....A.E.ELTF
Retrocopy ANVEEASFLRFQNSIWKN-EEKMECVHPLQLVWDPLSSALKHNKPVKNDL-VNEAAI>XXXGAPEVELTF

Parental  LRSQIAAIVEMQELKNSTNSSSFGLNDEPISLGQLSSSQAAHLSVEPDQFPSSVL
          L.SQI.AIVEMQELKNSTNSSSFGLND.PISLGQ..SS.A..LS.E......S.L
Retrocopy LHSQIPAIVEMQELKNSTNSSSFGLNDGPISLGQMPSSGAVQLSGESHIYICSLL

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_1513 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000244	1 retrocopy	retro_cfam_1178,
Myotis lucifugus	ENSMLUG00000002331	1 retrocopy	retro_mluc_2227,
Monodelphis domestica	ENSMODG00000017453	1 retrocopy	retro_mdom_1813,
Nomascus leucogenys	ENSNLEG00000014793	1 retrocopy	retro_nleu_1513 ,
Pan troglodytes	ENSPTRG00000018634	1 retrocopy	retro_ptro_1491,