RetrogeneDB ID: retro_nleu_1077

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397280.1:807573..808380(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR3
• Ensembl ID: ENSNLEG00000011619
• Aliases: None
• Description: None

Sequence

>retro_nleu_1077
GCTACCTCCTGGACCACAAGACAAATAGGAGAATACATGTTGACTGGTAGGTTATAGACAAGTGGAAATGGTGTCACTCA
TGGCATTTCTGTGCCTGAAGGGTATGTGATTGGCTGCCGTATTAAATACATTCCAATTGCAGGATGAGCTATAACATATT
TTATTCAGCAACTACTGAGAGACCAAGAAGTAGGAATCCCTCCAGAGCAATCCCTGGAAACTGCTAAGGCAGTGAAGGAG
CACTATAGTTACGTCAGCTCAGATTTAGTAAAAGAATTTAAAAAGTAAGGTGCAGATGGGTCGCAGTGGATTTAAACAGT
ATATAAGAATCAATGCCATCTCAAATAAATAATTGTCCATTGATATTGGATATGACAGATTCTTGGGACCTGAAATCTTT
TTTCATCCAGGTTTGCTAATCCAGACTTTATACATCCCATCTCAGATGTTGCAGATGAAGTAATTCAGAATTGTTCTGTT
GATGTCAGACATCCTCTCAACAAGAATATTGTTGTCTATGGAGGTTCAACTGTGTTCAGGGACTTTGGACATCGCTTGCA
ATGAGATATGAAAAGAACTGTAGATGTCAGGCTGACCTTAAGTGAGGAATTAAGTAGCAGTAGATTGAAGCCAGAAGCTG
TTGATGTACAAGTCATTACACACCACATAGAGCAATATGCAATTTGGTTTGGAGGATCAATGCAGACTTCTCTGCTTGAG
TTCTATCAAGTATGCCACCCCCAAAAGGATTATAAAGAAATCGGACCTAGCATTTGTCATCACAATCTAGGGTTTGGAGT
CATGTCA

Alignment

ORF - retro_nleu_1077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.06 %
• Parental protein coverage: 64.27 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQ
          A.SWT.RQ.GE..LTG....SG.GVTH.I.V.EGYVIG..IK.IPIAG..ITYFIQQLLRD.EVGIPPEQ
Retrocopy ATSWTTRQIGEYMLTGRL*TSGNGVTHGISVPEGYVIGCRIKYIPIAG*AITYFIQQLLRDQEVGIPPEQ

Parental  SLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWI-KQYTGINAISKKEFSIDVGYERFLG-EIFFHP-EF
          SLETAKAVKE.YSYV..DLVKEF.K...DGS.WI.KQY..INAIS.K..SID.GY.RFLG.EIFFHP..F
Retrocopy SLETAKAVKEHYSYVSSDLVKEFKK*GADGSQWI>KQYIRINAISNK*LSIDIGYDRFLGPEIFFHP<RF

Parental  ANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGR
          ANPDF..PIS.V.DEVIQNC..DVR.PL.KNIV..GGST.FRDFG.RLQ.D.KRTVD.RL.LSEELS..R
Retrocopy ANPDFIHPISDVADEVIQNCSVDVRHPLNKNIVVYGGSTVFRDFGHRLQ*DMKRTVDVRLTLSEELSSSR

Parental  LKPKPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
          LKP...DVQVITHH...YA.WFGGSM..S..EFYQVCH..KDY.EIGPSIC.HN..FGVMS
Retrocopy LKPEAVDVQVITHHIEQYAIWFGGSMQTSLLEFYQVCHPQKDYKEIGPSICHHNLGFGVMS

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_1077 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003401	1 retrocopy	retro_btau_672,
Callithrix jacchus	ENSCJAG00000014091	4 retrocopies	retro_cjac_3602, retro_cjac_3813, retro_cjac_385, retro_cjac_4005,
Homo sapiens	ENSG00000115091	2 retrocopies	retro_hsap_1391, retro_hsap_4694,
Gorilla gorilla	ENSGGOG00000011346	1 retrocopy	retro_ggor_2921,
Mustela putorius furo	ENSMPUG00000010717	1 retrocopy	retro_mputfur_1275,
Mus musculus	ENSMUSG00000026341	1 retrocopy	retro_mmus_3653,
Nomascus leucogenys	ENSNLEG00000011619	2 retrocopies	retro_nleu_1077 , retro_nleu_2364,
Nomascus leucogenys	ENSNLEG00000015688	1 retrocopy	retro_nleu_733,
Pongo abelii	ENSPPYG00000012798	1 retrocopy	retro_pabe_3647,
Pan troglodytes	ENSPTRG00000012388	2 retrocopies	retro_ptro_3118, retro_ptro_955,
Vicugna pacos	ENSVPAG00000009479	1 retrocopy	retro_vpac_468,