RetrogeneDB ID: retro_tbel_3676

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_148225:17704..18893(+)
• 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_3676
GTTGAAAGGATTGTAGACAAGAGGAAGAATAAGCAAGGAAAATGGGAGTATCTTATCCAGTGGGAAGGCTATGGGAGCCC
AGAGGACACGTGGGAGCCAGAACACCACTTCTTGCACTGTGAGTTTATCGACGAGTTCAATGGGCTGCACATATCCAAGG
ACAAGAGGATCAGGCCAGGGAAACAGTCTAACACCTCCAAGCTCCTACGTGACAGCTGGAGCCCAGCGAGTGAAAAACTA
GCCCATAGACCTTCAGAACCTGGGAAGAGCAAAAGAACTTCCCATAAATGGAAGCACATCAACCCTCCCCTATCTGAGCC
AAAGAAGGGGTACTCAGGCAAGCCCCCTTCAGGGGGCGATCGAGCTGCCAAGATGGTGTCTTACAGGACTACCCCCAGCG
GTTTGTAAATAATGCCCCTGAAAAAGGCTCAGAATGGGATGGAAAATGGGGATGCCGGCTCTGAGAAGGATGAGAGGCAC
TTTGGACATGGGTCGCATCAGCCTGGCTTGGATTTGAATGATCATGTTGGAAAGCATGTGGGTGATTGTGAAGTGAACCA
TGCAGCACTGGCAGAGAATGGGCTTGGCCCTGCTCTGACTAATGAGGGATTGAACCTGCACAGCCCTGCGAAGAGAAAGC
TGGAAACAGAGAAGGACTATGTCTTTGACAAGATGCTCAGGTACAGCGTCCGCCAGAATGAAAGTCAACTGTCGGTTTTG
AAATATTGTCGTGCGGAAAGAAGAAGGGTTCACACACATCTTGCTGTCCAGCCAGACCTCGGATAACAATGCATTGACAC
CTGAGATCATGAAGGAAGTCCAGCGAGTGCTCTGCAATGCAGCCACAGATGACAGCAAACTGCTGCTTCTCAGTGCAGTG
GGGAGTGTGTTCTGCAGTGGCCTAGATTACTCCTACCTAATTGGGTGGTTGTCCAGCGACCAAAGAAAGGAGAGCACTCG
GATTGCCGAAGCCATCAGGGACTTTGTGAAGGCCTTTATCCAGTTTAAGAAACCCATTGTGGTGGCCATCAATGGGCCGG
CCCTGGGCCTGGGTGCCTCCATCCTACCCCTCTGTGACATCATGTGGGCCAATGAGAAGGCCTGGTTTTAGACGCCCTAC
GCCACCATCCGCCTCACACCTGCTGGCTGCTCATCCTACACCTTCCCCCAGATCCTGGGTGTGGCTCTG

Alignment

ORF - retro_tbel_3676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.23 %
• Parental protein coverage: 79.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VERIVDKRKNKKGKWEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNGLHVSKDKRIRPGKQSNTSKLL
          VERIVDKRKNK.GKWEYLI.W.GYGS.EDTWEPEHH.LHCE.FIDEFNGLH.SKDKRIRPGKQSNTSKLL
Retrocopy VERIVDKRKNKQGKWEYLIQWEGYGSPEDTWEPEHHFLHCE-FIDEFNGLHISKDKRIRPGKQSNTSKLL

Parental  RDSRSPASEKLAHRPSEPGKSKGTSHKRKRINPPLSKPKKGYSGKPPTGGDRAAKTVSYRTTPSGLQIMP
          RDS.SPASEKLAHRPSEPGKSK.TSHK.K.INPPLS.PKKGYSGKPP.GGDRAAK.VSYRTTPSGL.IMP
Retrocopy RDSWSPASEKLAHRPSEPGKSKRTSHKWKHINPPLSEPKKGYSGKPPSGGDRAAKMVSYRTTPSGL*IMP

Parental  LKR-QNGMENGDA-SEKDERHFGNGSHQPGLDLNDHVGEQDVGDCEVNHAALAENGLGSALTNGGLNLHS
          LK..QNGMENGDA.SEKDERHFG.GSHQPGLDLNDHVG...VGDCEVNHAALAENGLG.ALTN.GLNLHS
Retrocopy LKKAQNGMENGDAGSEKDERHFGHGSHQPGLDLNDHVGKH-VGDCEVNHAALAENGLGPALTNEGLNLHS

Parental  PVKRKLETEKDYVFDKRLRYSVRQNES-NCRFRDIVVRKEEGFTHILLSSQTSDNNALXXXIMKEVRRAL
          P.KRKLETEKDYVFDK.LRYSVRQNES.NCRF..IVVRKEEGFTHILLSSQTSDNNAL...IMKEV.R.L
Retrocopy PAKRKLETEKDYVFDKMLRYSVRQNES>NCRF*NIVVRKEEGFTHILLSSQTSDNNALTPEIMKEVQRVL

Parental  CNAATDDSKLLLLSAVGSVFCSGLDYSYLIGRLSSDRRKESTRIAEAIRDFVKAFIQFKKPIVVAINGPA
          CNAATDDSKLLLLSAVGSVFCSGLDYSYLIG.LSSD.RKESTRIAEAIRDFVKAFIQFKKPIVVAINGPA
Retrocopy CNAATDDSKLLLLSAVGSVFCSGLDYSYLIGWLSSDQRKESTRIAEAIRDFVKAFIQFKKPIVVAINGPA

Parental  LGLGASILPLCDIVWASEKAWFQTPYATIRLTPAGCSSYTFPQILGVAL
          LGLGASILPLCDI.WA.EKAWF.TPYATIRLTPAGCSSYTFPQILGVAL
Retrocopy LGLGASILPLCDIMWANEKAWF*TPYATIRLTPAGCSSYTFPQILGVAL

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_3676 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3676 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,