RetrogeneDB ID: retro_tbel_4160

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_69356:1..1098(-)
• 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_4160
AAGATTGTAAACAAGAGGAAGAATAAAAAGAAAAATGGGAGTACCTTATCCAGTGGAAAGGCTATGGGAGCACAGAGGAC
ACGTGGGAGCCAGAACACCACCTCTTGCACTGTGAGGAGTTTATCAACGAGTTCAATGGGCTGCACGTGTCCAAGGACAA
GAAGATCAGGCCAGGGAAACAGTCTAACACCTCCAAGCTCCTACGTGGCAGCCGGAGCCCACCGAGTGAGAAACTAGCCC
ATAGACCTTCAGAACCTAGGAAGAGCAAAGGGACTTCCCATAAACGGAAGCGCATCAACCCTCCCCTATCTAAGCCAAAG
AAGGGATACTCAGGCAAGCCCCCTGCAGGGGGCAATCGAGCTGCCAAGACGGTGTCTTACAGGACTACCCCCAGCGGTTT
GCAAATAATGCCCCTGAAAAAGTCTCAGAATGGGATGGAAAATAGGGACACCGGCTCTGAGAAGGACGGGAGGCACTTTG
GAAACGGGTTGCATCAGCCTGGCTTGGACTTGGACGATCATGTGGGAGAGCAGGATGTGGGTGATTGTGAAGTGAGCCCT
GCAGCACTGGCAGAGAACGGGCTCGGCTCTGCTCTGACTAATGGGGGATTGAACCTCCACAGCCCTGCGAAGAGAAAGCT
GGAAACAGAGAAGGACTATGTCTTTGACAAGAGGCTCATGTACAGCGTCCGCCAGAATGAAAGCAACTGTTGGTTTCAAA
ATATTGTCGTGCGGAAAGAAGAAGGGTTCACCCACATCTCGCTGTCCAGCCAGACCTCGGATAACAATGCACTGACACCT
GAGATCATGAAGGAAGTCTGGCGAGCGCTCTGCAATGCAGCCACAGATGACAGCAAACTGCTGCTCCTCAGTGCAGTGGG
GACTGTGTTCTGCAGCGGCCTAGATTACTCCTACCTAATTGGTCGGTTGTCCAGCGACCAAAGAAAGGAGAGCACTCGAA
TTGCCGAAGCCATCAGGGACTTTGTGAAGGCCTTTATCCAGTTTAAGAAACCCATTGTGGTGGCCATCAATGGGCCGGCC
CTGGGCCTGGGTGCCTCCATCCTACCCCTCTGTGACATCGTGTGGGCCAATGAGAAG

Alignment

ORF - retro_tbel_4160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.46 %
• Parental protein coverage: 73.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RIVDKRKNKKG-KWEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNGLHVSKDKRIRPGKQSNTSKLLR
          .IV.KRKNKK..KWEYLI.WKGYGSTEDTWEPEHHLLHCEEFI.EFNGLHVSKDK.IRPGKQSNTSKLLR
Retrocopy KIVNKRKNKKK<KWEYLIQWKGYGSTEDTWEPEHHLLHCEEFINEFNGLHVSKDKKIRPGKQSNTSKLLR

Parental  DSRSPASEKLAHRPSEPGKSKGTSHKRKRINPPLSKPKKGYSGKPPTGGDRAAKTVSYRTTPSGLQIMPL
          .SRSP.SEKLAHRPSEP.KSKGTSHKRKRINPPLSKPKKGYSGKPP.GG.RAAKTVSYRTTPSGLQIMPL
Retrocopy GSRSPPSEKLAHRPSEPRKSKGTSHKRKRINPPLSKPKKGYSGKPPAGGNRAAKTVSYRTTPSGLQIMPL

Parental  KR-QNGMENGDA-SEKDERHFGNGSHQPGLDLNDHVGEQDVGDCEVNHAALAENGLGSALTNGGLNLHSP
          K..QNGMEN.D..SEKD.RHFGNG.HQPGLDL.DHVGEQDVGDCEV..AALAENGLGSALTNGGLNLHSP
Retrocopy KKSQNGMENRDTGSEKDGRHFGNGLHQPGLDLDDHVGEQDVGDCEVSPAALAENGLGSALTNGGLNLHSP

Parental  VKRKLETEKDYVFDKRLRYSVRQNESNCRFRDIVVRKEEGFTHILLSSQTSDNNALXXXIMKEVRRALCN
          .KRKLETEKDYVFDKRL.YSVRQNESNC.F..IVVRKEEGFTHI.LSSQTSDNNAL...IMKEV.RALCN
Retrocopy AKRKLETEKDYVFDKRLMYSVRQNESNCWFQNIVVRKEEGFTHISLSSQTSDNNALTPEIMKEVWRALCN

Parental  AATDDSKLLLLSAVGSVFCSGLDYSYLIGRLSSDRRKESTRIAEAIRDFVKAFIQFKKPIVVAINGPALG
          AATDDSKLLLLSAVG.VFCSGLDYSYLIGRLSSD.RKESTRIAEAIRDFVKAFIQFKKPIVVAINGPALG
Retrocopy AATDDSKLLLLSAVGTVFCSGLDYSYLIGRLSSDQRKESTRIAEAIRDFVKAFIQFKKPIVVAINGPALG

Parental  LGASILPLCDIVWASEK
          LGASILPLCDIVWA.EK
Retrocopy LGASILPLCDIVWANEK

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_4160 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4160 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,