RetrogeneDB ID: retro_nleu_2724

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397410.1:1291648..1292336(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YTHDF1
• Ensembl ID: ENSNLEG00000009975
• Aliases: None
• Description: None

Sequence

>retro_nleu_2724
AGCATGGACACTTAGAGAACAAAAGGACAAGATAATAAAGTACACAATGATTCTTTGCATCACAAGGATGTGGGTCATGA
CAATGACTTTCAGTCCTACCTTTCTGGAGAGTCAAATTAGAGTAACAATTACCCTTCAGTGAGTGACCTCTACCTGTCCA
GCTATTACCCACCATCCACTGGAGTTCCTTAATCCCTCAATGAGGCTCTGTGGTCCACTGCAAGGGACCCTTTGATTCTA
CACCTCATCACCTATGAACAGCTCAGTAACAGAGATCATAATTTTATGCACAATTCTATTTTGGGATAGCCTTGGGGTCT
GGAGAACAAAATCTATCAGCACAGGTTTAATTTTTACCCCCAAACCTTATATTATTGGCATGGAGGACAAGTGGGTCTCA
AGGGTAGCAGATTCAGAGCTCTACATATGGGAGCAGCTACACCTACTCCCAAGCTCCCTGGGCCACACAGTGGTTGATGG
GCAGATGGGCTTTCACAGTGACACCCTTAGCAAGGCCCCTGGAGTGAACAGCCTGAAGCAGGGCATGGTCAGCCTGAAGA
TTGGGGATGTCAGCTCCTCTGCAGTCAAGACAATGTGCTCTGTCATCAGCAGCGTGGCACTGATTGGCATCCTTTCTGGC
AATGATGGGACATATGTGAACATGGCAGTTTCAAAGCTGACCTCATGG

Alignment

ORF - retro_nleu_2724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.28 %
• Parental protein coverage: 98.28 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVDTQRTKGQDNKVQNGSLHQKDTVHDNDFEPYLTGQSNQSNSYPSMSDPYLSSYYPPSIGFPYSLNEAP
          S.DT.RTKGQDNKV.N.SLH.KD..HDNDF..YL.G.SN.SN.YPS.SD.YLSSYYPPS.G.P.SLNEA.
Retrocopy SMDT*RTKGQDNKVHNDSLHHKDVGHDNDFQSYLSGESN*SNNYPSVSDLYLSSYYPPSTGVP*SLNEAL

Parental  WSTAGDPPIPYLTTYGQLSNGDHHFMHDAVFGQPGGLGNNIYQHRFNFFPE-NPAFSAWGTSGSQGQQTQ
          WSTA.DP.I..L.TY.QLSN.DH.FMH....G.P.GL.N.IYQHRFNF.P..N....AW.TSGSQG.Q.Q
Retrocopy WSTARDPLILHLITYEQLSNRDHNFMHNSILG*PWGLENKIYQHRFNFYPQ<NLILLAWRTSGSQG*QIQ

Parental  SSAYGSSYTYP-PSSLGGTVVDGQPGFHSDTLSKAPGMNSLEQGMVGLKIGDVSSSAVKTVGSVVSSVAL
          SS.YGSSYTY..PSSLG.TVVDGQ.GFHSDTLSKAPG.NSL.QGMV.LKIGDVSSSAVKT..SV.SSVAL
Retrocopy SSTYGSSYTYS<PSSLGHTVVDGQMGFHSDTLSKAPGVNSLKQGMVSLKIGDVSSSAVKTMCSVISSVAL

Parental  TGVLSGN-GTNVNMPVSKPTSW
          .G.LSGN.GT.VNM.VSK.TSW
Retrocopy IGILSGNDGTYVNMAVSKLTSW

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_2724 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	ENSG00000149658	1 retrocopy	retro_hsap_3220,
Gorilla gorilla	ENSGGOG00000008340	1 retrocopy	retro_ggor_2186,
Nomascus leucogenys	ENSNLEG00000009975	1 retrocopy	retro_nleu_2724 ,
Pan troglodytes	ENSPTRG00000013730	1 retrocopy	retro_ptro_2170,