RetrogeneDB ID: retro_tbel_4710

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_98417:12973..14124(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDYL2
• Ensembl ID: ENSTBEG00000000034
• Aliases: None
• Description: chromodomain protein, Y-like 2 [Source:HGNC Symbol;Acc:23030]

Sequence

>retro_tbel_4710
TGGAAGTATCTTATCCGGTGGAAAGGCTATGGGAGCACAAAGGACATGTGGGAGCCAGAACACCATCTCTTGCACTGTGA
GGAGTTTATCAATGAGTTCAATGGGCTGCACGTAGCCAAGGACAAGAGGATCAGGCCAGGGAAACAGTCTAACACCTCCA
AGTTCCTACGTGACAGCTGGAGCCCAGTGAGTGAAAAACTAGCCCATAGACCTTCAGAACCTGGGAAGAGCAAAGGGACT
TCCCATAAACGGAAGTGCATCAACCCTCCCCTATCTAAGCCAAAGAAGGGGTACTCAGACAAGCCCCCTGCAGGGGCGAT
CGAGCTGCCAAGATGGTGTCTTACAGGACTACCCCCAGCGGTTTGGAAATAATGCCCCTGAAAAAGGCTCAGAATGGGAT
GGAAAATGGGGACGCCGGCTCTGAGAAGGACGAGAGGTACTTTGGAAACGGGTCGCATCAGCCTGGCTTGGACTTGAATG
ATCATGTTGGAGAGCAAGATGTGGGTGATTGTGAAGTGAGCCGTGCAGCACTGGCAGAGAACGGGCTCGGCTCTGCTCTG
ACTAATGGGGGATTGAACCTCCACAGCCCTGCGAAGAGAAAGCTGGAAACAGAGAAGGACTATGTCTTTGACAAGAGGCT
CATGTACAGCGTCCGCCAGAATGAAAGCAACTGTTGGTTTCAAAATATTGTCGTGCGGAAAGAAGAAGGGTTCACACACA
TCTCGCTGTCCAGCCAGACCTCGGATAACAATGCACTGACACCTGAGATCATGAAGGAAGTCCGGCGAGCGCTCTGCAAT
GCAGCCACAGATGACAGCAAACCGCTGCTCCTCAGTGCAGTGGGGACTGTGTTCTGCAGCGGCCTAGATTACTCCTACCT
AATTGGTCGGTTGTCCAGCGACCAAAGAAAGGAGAGCACTCGAATTGCCAAAGCCATCAGGGACTTTGTGAAGGCCTTTA
TCCAGTTTAAGAAACCCATTGTGGTGGCCATCAATGGGCCGGCCCTGGGCCTGGGTGCCTCCATCCTACCCCTCTGTGAC
ATCGTGTGGGCCAATGAGAAGGCCTGGTTTCAGACGCCCTATGCCACCATCCGCCTCACACCCACTGGCTGCTCATCCTA
CACCTTCCCCCAGATCCTGGGTGTGGCTCTG

Alignment

ORF - retro_tbel_4710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 77.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNGLHVSKDKRIRPGKQSNTSKLLRDSRSPASEKLAHR
          W.YLIRWKGYGST.D.WEPEHHLLHCEEFI.EFNGLHV.KDKRIRPGKQSNTSK.LRDS.SP.SEKLAHR
Retrocopy WKYLIRWKGYGSTKDMWEPEHHLLHCEEFINEFNGLHVAKDKRIRPGKQSNTSKFLRDSWSPVSEKLAHR

Parental  PSEPGKSKGTSHKRKRINPPLSKPKKGYSGKPPTG-GDRAAKTVSYRTTPSGLQIMPLKR-QNGMENGDA
          PSEPGKSKGTSHKRK.INPPLSKPKKGYS.KPP.G.GDRAAK.VSYRTTPSGL.IMPLK..QNGMENGDA
Retrocopy PSEPGKSKGTSHKRKCINPPLSKPKKGYSDKPPAG<GDRAAKMVSYRTTPSGLEIMPLKKAQNGMENGDA

Parental  -SEKDERHFGNGSHQPGLDLNDHVGEQDVGDCEVNHAALAENGLGSALTNGGLNLHSPVKRKLETEKDYV
          .SEKDER.FGNGSHQPGLDLNDHVGEQDVGDCEV..AALAENGLGSALTNGGLNLHSP.KRKLETEKDYV
Retrocopy GSEKDERYFGNGSHQPGLDLNDHVGEQDVGDCEVSRAALAENGLGSALTNGGLNLHSPAKRKLETEKDYV

Parental  FDKRLRYSVRQNESNCRFRDIVVRKEEGFTHILLSSQTSDNNALXXXIMKEVRRALCNAATDDSKLLLLS
          FDKRL.YSVRQNESNC.F..IVVRKEEGFTHI.LSSQTSDNNAL...IMKEVRRALCNAATDDSK.LLLS
Retrocopy FDKRLMYSVRQNESNCWFQNIVVRKEEGFTHISLSSQTSDNNALTPEIMKEVRRALCNAATDDSKPLLLS

Parental  AVGSVFCSGLDYSYLIGRLSSDRRKESTRIAEAIRDFVKAFIQFKKPIVVAINGPALGLGASILPLCDIV
          AVG.VFCSGLDYSYLIGRLSSD.RKESTRIA.AIRDFVKAFIQFKKPIVVAINGPALGLGASILPLCDIV
Retrocopy AVGTVFCSGLDYSYLIGRLSSDQRKESTRIAKAIRDFVKAFIQFKKPIVVAINGPALGLGASILPLCDIV

Parental  WASEKAWFQTPYATIRLTPAGCSSYTFPQILGVAL
          WA.EKAWFQTPYATIRLTP.GCSSYTFPQILGVAL
Retrocopy WANEKAWFQTPYATIRLTPTGCSSYTFPQILGVAL

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_4710 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4710 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 3 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000000034	5 retrocopies	retro_tbel_1040, retro_tbel_3676, retro_tbel_4160, retro_tbel_4448, retro_tbel_4710 ,
Tupaia belangeri	ENSTBEG00000008062	1 retrocopy	retro_tbel_4165,
Tupaia belangeri	ENSTBEG00000015862	2 retrocopies	retro_tbel_2398, retro_tbel_814,