RetrogeneDB ID: retro_nleu_2323

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397343.1:4945483..4946538(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFB2M
• Ensembl ID: ENSNLEG00000004146
• Aliases: None
• Description: None

Sequence

>retro_nleu_2323
CTGTCCGACTCCTGTCCGCAGCTGTGGCCGGATCCGGATTTCAGGAACCCGCCAAGGCAGGTGTCTAACTCCAGCTTAGA
CTTTGAGCGTTGCGTAGCCAACCGGAGATTGGCTGAGACCCTGGCGCAAATCGTATGGAGAAAACAAAATAGACCTCCAC
ACCTATTGCTGCAGTGCAGTCCAGGTCCTGGAATCCTGACTCAGGCATTACTTGAAGTTGGTGCCAAAGTGGTTGCCCTT
GAAAGTGACAAAACTTTTATTCCACATTTGGAGTCCTTAGGAAAAAATCTGGATGGAAAACTACAAGTGATTCACTGTGA
CTTCTTTAAAATAGATCCTAGAAGTGGTGGAGTAATAAAACCACCCGCTATGGCTTCTCAAGGGCTCTTTCAGAATTTGG
GAATAGAAGCAGTTCCTTGGACAGCAGGCAGCCCTTTAAAAGTAACTGGAATGTTCTCAAGTAGAGGTGAAAAAAGGGCC
ACTTTGGAAACCTGCATATGACATATTCCTGTACTTCTATATATAAATTTGGACGAATAGAACTAAATATGTTTATTGGT
GAAAAAGAATTCCAGAAACTAACGGCAGATCCCCGAAATCCAGACTTGTATCATATATGAAGTGTTATCTGGCAAGTAGC
TTGTGAGATTAAGGTTCTGCACATGGAGCCTTGGTCATCATTTGATGTATACACCCAAAATGGGCGTCTGGAAAACCCAA
AGCGTAGGGAATTATTAGAACTATGACAACAAAATCTGTATCTTATTCAAATGACTCCTCATGGAAATTTATTTACCGAG
AACTTAACACCTATTAACTATAATATATTTTTTCACACGTTAAAGCACTGTTTTGGAAGGCGCAGTGCCAGTCTAATAGA
CCACTTACATTCATTGAGTCGACTTGATGCAATGGATATATTGATGCAAATAGGAAAAAAGGAAGAAGAGAAAATAACTA
ACGTGTACCCTCACGACTTCAAAAAACTTTTTGAAACTATGGAGTGTTCCAAAGACTGTGCTTATAAATGGCTGTACGAT
GAAACCCTGGAAGAT

Alignment

ORF - retro_nleu_2323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.59 %
• Parental protein coverage: 95.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSDSSPELWPEPDFRNPPKKASKSKLDFKRYVTDRRLAETLAQIVWGKPNRPPHLLLECNPGPGILTQAL
          LSDS.P.LWP.PDFRNPP...S.S.LDF.R.V..RRLAETLAQIVW.K.NRPPHLLL.C.PGPGILTQAL
Retrocopy LSDSCPQLWPDPDFRNPPRQVSNSSLDFERCVANRRLAETLAQIVWRKQNRPPHLLLQCSPGPGILTQAL

Parental  LEAGAKVVALESDKTFIPHLESLGRNLDGKLRVIHCDFFKIDPRSGGLIKPPAMSSRGLFKNLGIEAVPW
          LE.GAKVVALESDKTFIPHLESLG.NLDGKL.VIHCDFFKIDPRSGG.IKPPAM.S.GLF.NLGIEAVPW
Retrocopy LEVGAKVVALESDKTFIPHLESLGKNLDGKLQVIHCDFFKIDPRSGGVIKPPAMASQGLFQNLGIEAVPW

Parental  TADIPLKVIGMFPSRGEKRALWKLA-YDLYSCTSIYKFGRIEVNMFIGEKEFQKLMADPRNPDLYHVLSV
          TA..PLKV.GMF.SRGEKRA.........YSCTSIYKFGRIE.NMFIGEKEFQKL.ADPRNPDLYH..SV
Retrocopy TAGSPLKVTGMFSSRGEKRATLETC<HMTYSCTSIYKFGRIELNMFIGEKEFQKLTADPRNPDLYHI*SV

Parental  IWQVACEIKVLHMEPWSSFDVYTRKGRLENPKRRELLDLLQQKLYLIQMTPRQNLFAKSLTPMNYNIFFH
          IWQVACEIKVLHMEPWSSFDVYT..GRLENPKRRELL.L.QQ.LYLIQMTP..NLF...LTP.NYNIFFH
Retrocopy IWQVACEIKVLHMEPWSSFDVYTQNGRLENPKRRELLEL*QQNLYLIQMTPHGNLFTENLTPINYNIFFH

Parental  LLKHCFGRRSATVIDHLRSLTPLDARDILMQIGKKEDEKVVNMYPQDFKTLFETIECSKDCAYKWLYDET
          .LKHCFGRRSA..IDHL.SL..LDA.DILMQIGKKE.EK..N.YP.DFK.LFET.ECSKDCAYKWLYDET
Retrocopy TLKHCFGRRSASLIDHLHSLSRLDAMDILMQIGKKEEEKITNVYPHDFKKLFETMECSKDCAYKWLYDET

Parental  LED
          LED
Retrocopy LED

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_2323 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013225	1 retrocopy	retro_cpor_451,
Homo sapiens	ENSG00000162851	1 retrocopy	retro_hsap_3548,
Gorilla gorilla	ENSGGOG00000001095	1 retrocopy	retro_ggor_2396,
Myotis lucifugus	ENSMLUG00000003923	1 retrocopy	retro_mluc_1302,
Macaca mulatta	ENSMMUG00000022915	1 retrocopy	retro_mmul_1814,
Nomascus leucogenys	ENSNLEG00000004146	1 retrocopy	retro_nleu_2323 ,
Oryctolagus cuniculus	ENSOCUG00000013727	2 retrocopies	retro_ocun_1557, retro_ocun_236,
Otolemur garnettii	ENSOGAG00000007823	2 retrocopies	retro_ogar_1444, retro_ogar_2187,
Pongo abelii	ENSPPYG00000000046	1 retrocopy	retro_pabe_3039,
Pan troglodytes	ENSPTRG00000002188	1 retrocopy	retro_ptro_2412,