RetrogeneDB ID: retro_nleu_1688

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397304.1:3165561..3166523(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTA3
• Ensembl ID: ENSNLEG00000016680
• Aliases: None
• Description: None

Sequence

>retro_nleu_1688
CTTTCTTTGTCACCCCAACATGAATCCTTGCCTTCAACACATATTAGGGGAAAATGCAGTGTTGCCTTATGAATTAGACA
GAATCAGTATTGCATATCTTCATAAAAAGTATACTTTCTTCTACTTATTGATCATGACCCCTCATCGAAAACACTATTAG
CTGATGAAGGTGAATTCAGAATGGGACCTAGATATCAAGTAGATGTCCCAGAAATGCTCATAGAAGGAGAATCAGATGAG
AGAGAACAGTGAAAATGGAAAGTTAAAGTTTGGGGATCCAAATAGCCCACTTAAGGATTGATCAATTAACCAGTTTTTAA
TTGTAGCAAGTACTATTGGGACCCTCCCTAGACCCCTCGATTGCAGCAGTTCTTTGAGGCAGCCTAGTTTGCATATGAGT
GCTGCTGCAGCTTCCCAAGACATCACCTTCTTTCATGCTATTGATACAATGTGTAGACACAGCTATGATTTGAGCAGTGC
AATTAGTGTCTCAGTACCACTTGAAGAAGCTGTTTTATGCAGAGATAAAATGGAAGAATGGTCAGCCTCTTAAGCTAGCT
TATTTGAAGAGGTACTGGAAAAAATATGGCAAAGACTTCAATGACATATGCCAAAACTTTTTCCCTTGGAAATCATTGAG
TAGCATCACTGAATGTTATTTCTTGTGGAGAACTACTGACAGATATGTGCAACAGAAATGGTTAAAAGCGGCAGAAAATG
AGAGTAAGCTGAAACAAGTATATATCCCAATTTACAGCAAACCAAATCCCAACCAAATATCTACCAGCAATGGCAAGCCT
GGTGCTGTGAGTGGAACCATGAGGATGACATTCCTGCCTCAGAATCCCCTTTTGGTGCAAGCCTGGGAGGGCTGCTGTGC
TACATAGTCTAACCAGTAGTATTCTTGGGGCCTACCTAATATGCAGTGCAATTTGTTGGCTTTATTAAGAAAAATATGGA
GA

Alignment

ORF - retro_nleu_1688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.01 %
• Parental protein coverage: 53.96 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LFLSRQYESLPATHIRGKCSVAL-LNETESVL-SYLDKEDTFFYSLV-YDPSLKTLLADKGEIRVGPRYQ
          L.LS.Q.ESLP.THIRGKCSVAL..N.TESVL..YL.K..TFFY.L...DPS.KTLLAD.GE.R.GPRYQ
Retrocopy LSLSPQHESLPSTHIRGKCSVAL<MN*TESVL<AYLHKKYTFFYLLI<HDPSSKTLLADEGEFRMGPRYQ

Parental  ADIPEMLLEGESDEREQSKLEVKVW-DPNSPLTDRQIDQFLVVARAVGTFARALDCSSSVRQPSLHMSAA
          .D.PEML.EGESDEREQ.K..VKVW.DPNSPL.D..I.QFL.VA...GT..R.LDCSSS.RQPSLHMSAA
Retrocopy VDVPEMLIEGESDEREQ*KWKVKVW>DPNSPLKD*SINQFLIVASTIGTLPRPLDCSSSLRQPSLHMSAA

Parental  AASRDITLFHAMDTLYRHSYDLSSAISVLVPLGGPVLCRDEMEEWSASEASLFEEALE-KYGKDFNDIRQ
          AAS.DIT.FHA.DT..RHSYDLSSAISV.VPL...VLCRD.MEEWSAS.ASLFEE.LE.KYGKDFNDI.Q
Retrocopy AASQDITFFHAIDTMCRHSYDLSSAISVSVPLEEAVLCRDKMEEWSAS*ASLFEEVLE>KYGKDFNDICQ

Parental  DFLPWKSLTSIIEYYYMWKTTDRYVQQKRLKAAEAESKLKQVYIPTY-KPNPNQISTSNGKPGAVNGAVG
          .F.PWKSL.SI.E.Y..W.TTDRYVQQK.LKAAE.ESKLKQVYIP.Y.KPNPNQISTSNGKPGAV.G...
Retrocopy NFFPWKSLSSITECYFLWRTTDRYVQQKWLKAAENESKLKQVYIPIYSKPNPNQISTSNGKPGAVSGTMR

Parental  TTFQPQNPLLGRACESCYATQSHQWYSWGPPNMQCRLCAICWLYWK
          .TF.PQNPLL..A.E.C.AT.S.Q.YSWG.PNMQC.L.A.....W.
Retrocopy MTFLPQNPLLVQAWEGCCAT*SNQ*YSWGLPNMQCNLLALLRKIWR

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_1688 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
Callithrix jacchus	ENSCJAG00000014614	1 retrocopy	retro_cjac_1177,
Homo sapiens	ENSG00000057935	1 retrocopy	retro_hsap_2337,
Gorilla gorilla	ENSGGOG00000006895	1 retrocopy	retro_ggor_1773,
Nomascus leucogenys	ENSNLEG00000016680	1 retrocopy	retro_nleu_1688 ,
Pan troglodytes	ENSPTRG00000011867	1 retrocopy	retro_ptro_1708,