RetrogeneDB ID: retro_tbel_688

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2751:306882..308641(-)
• Located in intron of: ENSTBEG00000010434

Retrocopy information

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

Parental gene information

• Parental gene symbol: PARP9
• Ensembl ID: ENSTBEG00000003867
• Aliases: None
• Description: poly (ADP-ribose) polymerase family, member 9 [Source:HGNC Symbol;Acc:24118]

Sequence

>retro_tbel_688
GCAGAGACTGACACGTTCAGAGAAAACTATAGTTGGAAAATTCCTATTACTCACAATGACTTCAAAATTTTAAAAAATAA
TGAAAGTCAGCTGAATGAAGTCCTTCGGCTTAAGTTTAACTGTGTCTCTACACTGGTCACTGTAACTCTGGAAGGTAACA
GAAAGTCTCTGCAGGCCTACAGAAAGATGCTGAGTCCTGGGCTAGAGTTATCTGTGTGGAAAGATGACCTCACCAGACAT
GCTGTTGATGCTGTGGTGAATGCAGCCAATGAAGACCTTCTGCATGGGGGAGGCCTGGCCCTGGCCCTAGTGAAAGCTGG
TGGCCCTGAAATCCAAGAAGAGAGCAGAAAATTTGTTGCCCAATATGGTAGAATATCAGCTGGTAACATAGGTGTCACTG
GAGCTGGGATGCTTCCCTGCAAAACGATTATCCATGCTGTCGGGCCTCGGTGGTTGTCGACTGAACATCAGAGATGCATT
AATGAGCTGCAATATGCCATTATAAATGTACTGAACTATGTTATCTTTGGAAATGTGAGCATTGAGACAGTAGCAATTCC
AGCCCTGAGCTCCGGAATTTTCCCAGTTCCCTCTGAATTTGTGCACACGGGTCATTGTAGAAACAATCTGGTCTTATTTC
CAAGAAAGGCAAGGAGTCAGTAAATTGAAAGAAATTCACCTGGTGAGCAATGAGGACCCTACTGTTGCTGCCTTTAAAGA
TGCTTCAGAATTCTTTTTAGGACCGACAGAGCAGGTCCTCCAGATGAGTCGAGAAGCCATCCCTCCTTCCAACATGATAG
TCATAAACAACCTAACTCTCCAGGTTCTTCAGGATCACATTGAATGGCAGAAAACAGATATGATTGTTAATTCTGTAAGC
CCATATAGTCTTAGAATTGGACCTGTGTCGAAGTCAATTCTACAACATGCAGGACCTGAAATGGAATGGGAATTTAAACA
AAAAACTAAATGGCTTCACGGTTCCCCACCAGTAGTAGTCACAAAAGGGTATAAGTTGTCCTGCCAATACATATGCCATG
TAATATGGCATACATCATATGCTCCCGATCAGATATTGAAAAATGCAGTGGGGGAGTGTTTGAAGAAATGCATCGAGCTA
AACAAAACTTCTATTTCCTTTCCTGCCCTTGGGACCGGAAGCATTAATATGAGGAAAGATAAAGCAGTGGAGATTATGTT
TGAAGAAGTTTTAAAATTTGCCAAAGACTGTGCAGAAAAAAAGCTAATAGTAAATTTTGTGATCTTTCCAGAAGAACTAG
AGATGTATAAGGTTTTCATAGCTGAAATGGAAAAGGCCAAGAAATGGAGTCTCAGCAATTATAGTGTCCTCCCATCCAGA
GAGGAGAGAGGAGAAAATCGTTTTGAAGCTAGTTCTTCTGTCATCAATCTAATGGGATACAAAAACGAAGAGATGTGTGA
GGCCAAACTGTGGATTGAAAGGCTACTGACCCTCTGGGACCACCACATCATTGAGAATAATCATATTCTCTACCTCGGGG
GAAAAGAACATGACATGTTGTCTCAGCTTCAGAAAACCTCAAGTGTCTCCATCTCAGAGATTATCAGTCCAGGAAAAGCG
CATTTAGAGATTAAAGGAGCCCAGGCTGATCTTATTGAGGTGGTTCTGAACATTGAACAAATGCTATGTGAGGTTCAGGA
GGAAGTAGCAAGAAAAAAGGAGCGAGGCCTTTGGAGCCTGTCAGGACAGTGTACTGATAAGAATGAAATGAAAGTATCA

Alignment

ORF - retro_tbel_688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.25 %
• Parental protein coverage: 69.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SETDTFRENYSWKIPITHNDFKILKNNESQLNEVLRLKFNCVSTLVSLTLEGNRKSLQVYRKMLSPGLEL
          .ETDTFRENYSWKIPITHNDFKILKNNESQLNEVLRLKFNCVSTLV..TLEGNRKSLQ.YRKMLSPGLEL
Retrocopy AETDTFRENYSWKIPITHNDFKILKNNESQLNEVLRLKFNCVSTLVTVTLEGNRKSLQAYRKMLSPGLEL

Parental  SVWKDDLTRHAVDVVVNAANEDLLHGGGLALALVKAGGPEIQEESRKFVAQYGRISAGNIGVTGAGMLPC
          SVWKDDLTRHAVD.VVNAANEDLLHGGGLALALVKAGGPEIQEESRKFVAQYGRISAGNIGVTGAGMLPC
Retrocopy SVWKDDLTRHAVDAVVNAANEDLLHGGGLALALVKAGGPEIQEESRKFVAQYGRISAGNIGVTGAGMLPC

Parental  KMIIHAVGPRWLSTEHQRCISELQCAIMNVLNYVIFGNVSIETVAIPALSSGIF-QFPLNLCTRVIVETI
          K.IIHAVGPRWLSTEHQRCI.ELQ.AI.NVLNYVIFGNVSIETVAIPALSSGIF.QFPLNLCTRVIVETI
Retrocopy KTIIHAVGPRWLSTEHQRCINELQYAIINVLNYVIFGNVSIETVAIPALSSGIF>QFPLNLCTRVIVETI

Parental  WSYFQERQGVSKLKEIHLVSNEDPTVAAFKDASELLLGPTEQVLQMSREAIPPSNMIVINNLTLQVLQDH
          WSYFQERQGVSKLKEIHLVSNEDPTVAAFKDASE..LGPTEQVLQMSREAIPPSNMIVINNLTLQVLQDH
Retrocopy WSYFQERQGVSKLKEIHLVSNEDPTVAAFKDASEFFLGPTEQVLQMSREAIPPSNMIVINNLTLQVLQDH

Parental  IEWQKTDMIVNSVSPYSLRIGPVSKSILQHAGPEMEWEFT-KTKWLHGSPPVVVTKGYKLSCQYICHVIW
          IEWQKTDMIVNSVSPYSLRIGPVSKSILQHAGPEMEWEF..KTKWLHGSPPVVVTKGYKLSCQYICHVIW
Retrocopy IEWQKTDMIVNSVSPYSLRIGPVSKSILQHAGPEMEWEFKQKTKWLHGSPPVVVTKGYKLSCQYICHVIW

Parental  HTSYAPDQILKNAVGECLKKCIELNKTSISFPARGTGNINMRKDKAVEIMFEEVLKFAKDCAEKKLIVNF
          HTSYAPDQILKNAVGECLKKCIELNKTSISFPA.GTG.INMRKDKAVEIMFEEVLKFAKDCAEKKLIVNF
Retrocopy HTSYAPDQILKNAVGECLKKCIELNKTSISFPALGTGSINMRKDKAVEIMFEEVLKFAKDCAEKKLIVNF

Parental  VIFPEELETYKVFIAEMEKAKKWSLSNYSVLPSREERGENGFEASSSVINLMGFKNEEMCEAKLWIERLL
          VIFPEELE.YKVFIAEMEKAKKWSLSNYSVLPSREERGEN.FEASSSVINLMG.KNEEMCEAKLWIERLL
Retrocopy VIFPEELEMYKVFIAEMEKAKKWSLSNYSVLPSREERGENRFEASSSVINLMGYKNEEMCEAKLWIERLL

Parental  TLRDHHIIENNHILYLGGKEHDMLSQLQKTSSVSISEIISPGKAYLEIKGAQADLIEVVLNIEQMLCEVQ
          TL.DHHIIENNHILYLGGKEHDMLSQLQKTSSVSISEIISPGKA.LEIKGAQADLIEVVLNIEQMLCEVQ
Retrocopy TLWDHHIIENNHILYLGGKEHDMLSQLQKTSSVSISEIISPGKAHLEIKGAQADLIEVVLNIEQMLCEVQ

Parental  EEVARKKERGLWSLSGQCTDKNEMKES
          EEVARKKERGLWSLSGQCTDKNEMK.S
Retrocopy EEVARKKERGLWSLSGQCTDKNEMKVS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_688 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_688 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000003867	1 retrocopy	retro_tbel_688 ,