RetrogeneDB ID: retro_tbel_1811

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5804:46512..47332(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC3
• Ensembl ID: ENSTBEG00000007520
• Aliases: None
• Description: histone deacetylase 3 [Source:HGNC Symbol;Acc:4854]

Sequence

>retro_tbel_1811
CCGGTATTCAATGGCCTGTTTGAGTTCTCTCTGTCTACTGGCAGCTCCATGGCAAGCACTGTGAAACTTAATAAGCAGCA
GATGACATCATTGTGAATTGGGCTGGGGGCCTGTGCCATGCAAAGAAGTCTGAAGCATCTGGCTTCTGTTACATCAGTGA
TATTGTCTTGGCCATCCTGGAACTGCTAAAGCATCACCAGAGGGTGCTGTATATTGACACTGACACTCACCATGGGGATG
GCTTGGAAGAGGCCTTCTATACCATAGACTGGGTCAGACCATGCCCTTTCATCAATACAGAGAATACTTTACAGGAACTG
GAGACTTACAGGATATCAGGGCTGGCAAAGGCTCATATTATGCCTTTAACTATCCACTCCAAGATGGGATGGATGATGAG
TCCTGTGAGGCCATTTTCAAGGCAGTCAGATCCGAAGTGATGGAGATATTCCAGCCCAGTGCGGTGGTCTTGCAGTGTGG
CTCAGACTCCTTGTCCAGAGACCGGTTAGGTTGCTTCAATTTGACCATCAAAGGGCATGCCAAGTGTGTGGAATTTGTAA
AGAGCTTTAACCTGCCTATGCTGATGCTGGGAGGTGGTGGCTACACCATTCATAATGTCGCCCAGTGCTGGACATATGAG
ACGGCAGTGGCCCTGGACACAGAGATCCCTAATGATCTTCCATGGAAAAACTACTTCGAATATTTTGGGCCAGATTTCAA
GCTTCACTTTAGTCCTTCCAGCATGACCAACCAGAACACTAATGAATACCTGGAGAAGATCAAACAGCTGCTGTTTGAGA
ACTTGCAGATGCTGCTTCAC

Alignment

ORF - retro_tbel_1811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.71 %
• Parental protein coverage: 82.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVFPGLFEFCSRYTGASLQGATQLNNKIC-DIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPR
          PVF.GLFEF.S..TG.S......LN.....DI..NWAGGL.HAKK.EASGFCY..DIV..ILELLK.H.R
Retrocopy PVFNGLFEF-SLSTGSSMASTVKLNKQQM<DIIVNWAGGLCHAKKSEASGFCYISDIVLAILELLKHHQR

Parental  VLYIDIDIHHGDGVQEAFYLTDRV-MTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSY
          VLYID.D.HHGDG..EAFY..D.V..T..FH.Y..YF..GTGD.....A..G.YY..N.PL.DG.DD.S.
Retrocopy VLYIDTDTHHGDGLEEAFYTIDWV<QTMPFHQYREYF-TGTGDLQDIRAGKGSYYAFNYPLQDGMDDESC

Parental  KHLFQPVINQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTVRN
          ...F..V...V....QP...VLQCG.DSL..DRLGCFNL.I.GH..CVE.VKSFN.P.L.LGGGGYT..N
Retrocopy EAIFKAVRSEVMEIFQPSAVVLQCGSDSLSRDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIHN

Parental  VARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQTIFENLKMLNH
          VA.CWTYET.......I...LP...YFEYF.PDF.LH...S....NQN...YL..I.Q..FENL.ML.H
Retrocopy VAQCWTYETAVALDTEIPNDLPWKNYFEYFGPDFKLHFSPSS-MTNQNTNEYLEKIKQLLFENLQMLLH

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_1811 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1811 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000008662	1 retrocopy	retro_mluc_642,
Macaca mulatta	ENSMMUG00000012588	1 retrocopy	retro_mmul_49,
Procavia capensis	ENSPCAG00000010817	1 retrocopy	retro_pcap_298,
Ictidomys tridecemlineatus	ENSSTOG00000016240	1 retrocopy	retro_itri_1661,
Tupaia belangeri	ENSTBEG00000007520	1 retrocopy	retro_tbel_1811 ,