RetrogeneDB ID: retro_nleu_1834

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397312.1:16263027..16264022(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTBP1
• Ensembl ID: ENSNLEG00000000864
• Aliases: None
• Description: None

Sequence

>retro_nleu_1834
ATGGACGGCATTGTCCCAGAAATAGCAGTTGGTACAAAGCGGGGATCTGATGAGCTTTTCTCTACTTGTGTCACTAACAG
ACCATTTATCATGAGCAGCAACTCAGCCTCTGCACCAAATGGACATGGCAGCAAGAAGTTCAAAGGTGACAGCAGAAGCG
CCGGTGTCCCCTCCAGAGTGACCCACATCCAGAAGCTCCCATCGGCGTCACCGAAGGGGAGGTGATCTCCCTGGAGCTGC
CCTTTGGGAAGGTCACTAATCTCCTGATGCTGAAGGGGAAAAACCAGGCCTTCATCGAGTTGAGCACGGAGGAGGCTGCC
AACAGCGTGGTGAACTACTATCCCTCGGTGACGCCCGTGCTGCATGGCCAGCCCATCTACATCCAGTTCTCCAGCCACAA
GGGGCTGAAGACCGACAGCTCTCCCAACCAGGCGCGGGACCCGGCGGGCCCTCAGCCGTGAACTCGGTCCAGTCGGGGAA
CCTGGCCTTGACGGCCCCGGCGGCGGTCGTAGACGCAGGAATGGCCATGGCCGGGCAGAGCCCGGTGCTCGGGATCATCG
TGGAGAACCTCTTTTACCCCGTGACCCTGGATGTGCTGCACCAGATTTTCTCCAAGTTCGGCAAAGTGAAGACCATCACC
TTCATCAAGGACAACCAGTTCCAAGCTCTGCTGCAGTATGCGGACCCCGAGAACGCCCAGCATGCCAAGCTGTAGCTGCA
CCGGCAGAACACCTATAACGCCTGCCATACGCTGTGCATTGACTTCTCCAAGCTCATCAGCCTCAACGTCAAGTACAACA
ACTGCAAGAGCAGCGACTACCACGCCCAGACCTGCCCTCCGGGTACAGCCAGCCCTTGCTGGACCAGACATGGCCGCGGC
CTTCAATCTTTCAGTTCCCAACATCCATGGAGCCCTGGTCCCCCTGGCCATCCCCTTGGCGGTGGCGGCAGCTGCAGCAG
CAGGCCGGATCTCCATCCCGGGCCTGGCGGGGGCA

Alignment

ORF - retro_nleu_1834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.56 %
• Parental protein coverage: 59.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LHSIVPDIAVGTKVGISHFASPCVTNGPFIMSSNSASAANGNDSKKFKGDSRSAGVPSRVIHIRKLP-ID
          ...IVP.IAVGTK.G.....S.CVTN.PFIMSSNSASA.NG..SKKFKGDSRSAGVPSRV.HI.KLP.I.
Retrocopy MDGIVPEIAVGTKRGSDELFSTCVTNRPFIMSSNSASAPNGHGSKKFKGDSRSAGVPSRVTHIQKLP<IG

Parental  VTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD
          VTEGEVISL.LPFGKVTNLLMLKGKNQAFIE..TEEAAN..VNYY.SVTPVL.GQPIYIQFS.HK.LKTD
Retrocopy VTEGEVISLELPFGKVTNLLMLKGKNQAFIELSTEEAANSVVNYYPSVTPVLHGQPIYIQFSSHKGLKTD

Parental  SSPNQARAQAALQ-AVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFG
          SSPNQAR..A..Q.AVNSVQSGNLAL.A.AA.VDAGMAMAGQSPVL.IIVENLFYPVTLDVLHQIFSKFG
Retrocopy SSPNQARDPAGPQ<AVNSVQSGNLALTAPAAVVDAGMAMAGQSPVLGIIVENLFYPVTLDVLHQIFSKFG

Parental  TVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDY-TR
          .V.K.ITF.K.NQFQALLQYADP..AQHAKL.L..QN.YNAC.TL.IDFSKL.SLNVKYNN.KS.DY..R
Retrocopy KV-KTITFIKDNQFQALLQYADPENAQHAKL*LHRQNTYNACHTLCIDFSKLISLNVKYNNCKSSDY<PR

Parental  PDLPSGDSQPSLDQT-MAAAFGAPGIISASPYAGAGFPPTFAIPQAAG-LSVPNVHGA
          PDLPSG.SQP.LDQT.MAAAF................P...A...AAG..S.P...GA
Retrocopy PDLPSGYSQPLLDQT<MAAAFNLSVPNIHGALVPLAIPLAVAAAAAAGRISIPGLAGA

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_1834 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 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020162	1 retrocopy	retro_cjac_1901,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Equus caballus	ENSECAG00000018845	1 retrocopy	retro_ecab_330,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573,
Homo sapiens	ENSG00000011304	1 retrocopy	retro_hsap_1354,
Gorilla gorilla	ENSGGOG00000005090	1 retrocopy	retro_ggor_1054,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Nomascus leucogenys	ENSNLEG00000000864	1 retrocopy	retro_nleu_1834 ,
Nomascus leucogenys	ENSNLEG00000014696	1 retrocopy	retro_nleu_2327,
Pongo abelii	ENSPPYG00000009289	1 retrocopy	retro_pabe_1122,
Pan troglodytes	ENSPTRG00000010165	1 retrocopy	retro_ptro_928,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478,