RetrogeneDB ID: retro_nleu_1910

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397315.1:767517..768354(-)
• Located in intron of: ENSNLEG00000001773

Retrocopy information

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

Parental gene information

• Parental gene symbol: MIOX
• Ensembl ID: ENSNLEG00000000729
• Aliases: None
• Description: None

Sequence

>retro_nleu_1910
GTGAAGGTGACAGTGGACCCAGACCCTTCCCTGGTCTACCGATCTGAAGTGGACCCAGAGGCTGCCAAAGACAAGGCCGG
CTTCCAGAACTACGTGTTGGGTCCCCTCCTGGACCATGTCTTTACCACCTACAAGCTCATGCACATGCACCACACAGTGG
ATTTCGTCAGGAGCAAGCACGCCTGGTTTGGGGACTTTTCCTACAAGAAAATGAAGGTCGTGGAGCCCGTGGACCTGGTA
CATGGGCTGGTGGACGAATCAGACTCAGGCGTAGACTCCCCCACTCCTTCCAAGCCTTCCAGATGGCGGAGGACATCGGA
AAAGGTCACCCAGGCAAGGACTGGTTCCAGCTTGTTGGGCTTCTATGACCTAGGGAAGGTCCTGGCCCTGTTAGGGGAGC
CCCAGTGGGCGATCGTTGGAGACACATTCCCTGTTGGATGCTGTCCCCAGACCTCCGTGGTTTTGTAACTCCACTTTTCA
GGACAATCCCGACCTCCAGGATCCTCGATACAGCACAAAACTGGGCATGTATTAGCCCCACTGTGGGCTCGGCAGGGTCC
TCATGTCCTGGGGCCATAATGAGTACTTGTACCAGGTGATGATGTTCAACAAGTTCTCGCTCCCACTGGAGGCTTCCTAC
AAGATCCGATTCCACTCCTTCTGCCCTGGCACACAGGCGGTGACTACTAGCAGTGGTGCAGCAAGCAGGACCTGGCCATG
CTGCCCTGGGTCCAGGAGTTCAATTTGACCAACTTCCCTGACCTGCCAGACGTGGACAAGCTGCAGCCCTACTACCAGGG
GCTCATTGATAAGTACTGCCCTGGCATCCTAAGCTGG

Alignment

ORF - retro_nleu_1910 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MKVTVGPDPSLVYRPDVDPEVAKDKASFRNYTSGPLLDRVFTTYKLMHTHQTVDFVRSKHAQFGGFSYKK
          .KVTV.PDPSLVYR..VDPE.AKDKA.F.NY..GPLLD.VFTTYKLMH.H.TVDFVRSKHA.FG.FSYKK
Retrocopy VKVTVDPDPSLVYRSEVDPEAAKDKAGFQNYVLGPLLDHVFTTYKLMHMHHTVDFVRSKHAWFGDFSYKK

Parental  MTVMEAVDLLDGLVDESDPDVD-FPNSFHAFQTAEGIRKAHPDKDWFH-LVGLLHDLGKVLALFGEPQWA
          M.V.E.VDL..GLVDESD..VD..P.SF.AFQ.AE.I.K.HP.KDWF..L.G...DLGKVLAL.GEPQWA
Retrocopy MKVVEPVDLVHGLVDESDSGVD<LPHSFQAFQMAEDIGKGHPGKDWFQ>LLGF-YDLGKVLALLGEPQWA

Parental  VVGDTFPVGCRPQASVV-FCDSTFQDNP-DLQDPRYSTELGMYQPHCGLDRVLMSWGHDEYMYQVMKFNK
          .VGDTFPVGC.PQ.SVV.F....F...P.DLQDPRYST.LGMY.PHCGL.RVLMSWGH.EY.YQVM.FNK
Retrocopy IVGDTFPVGCCPQTSVV<FVTPLFRTIP<DLQDPRYSTKLGMY*PHCGLGRVLMSWGHNEYLYQVMMFNK

Parental  FSLPPEAFYMIRFHSF-YPWHTGRDYQQLCSQQDLAMLPWVQEFNKFDLYTKCPDLPDVDKLRPYYQGLI
          FSLP.EA.Y.IRFHSF..PWHTG.DY.Q.CS.QDLAMLPWVQEFN.....T..PDLPDVDKL.PYYQGLI
Retrocopy FSLPLEASYKIRFHSF<LPWHTGGDY*QWCSKQDLAMLPWVQEFN----LTNFPDLPDVDKLQPYYQGLI

Parental  DKYCPGILSW
          DKYCPGILSW
Retrocopy DKYCPGILSW

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_1910 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100253	1 retrocopy	retro_hsap_4087,
Gorilla gorilla	ENSGGOG00000013037	1 retrocopy	retro_ggor_2741,
Nomascus leucogenys	ENSNLEG00000000729	1 retrocopy	retro_nleu_1910 ,
Pan troglodytes	ENSPTRG00000014543	1 retrocopy	retro_ptro_2772,