RetrogeneDB ID: retro_tbel_707

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_281:73153..73840(-)
• Located in intron of: ENSTBEG00000010027

Retrocopy information

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

Parental gene information

• Parental gene symbol: TATDN1
• Ensembl ID: ENSTBEG00000006179
• Aliases: None
• Description: TatD DNase domain containing 1 [Source:HGNC Symbol;Acc:24220]

Sequence

>retro_tbel_707
ATGTTTTCCAGTACAGCTGGATGTCATCCTACAAGATGTGATGAATCTGAAAAGAATAACCCTGATCTTTACTTAATGGA
GTTGCTAGATCTTGCTGAAAACAGTAAGAGGAAAGTTGCAGCAATAGGGGAATATAGACTTGATTTTGACCGAATGCAGC
TTTGTTCCAAACATACTCAGCTCAAATATTTTGAAAATCAGTTCGAACTATCAGAACAAACAAAATTACCTATGTTTCTT
CATTGTGGAAACTCACACGATGAATTTTTGGACATAATGAAAAGAAATAGAGACCGGTAGTTGCTGGAGTGGTGCACTCG
TTTGACGGTACCAAGGAAGTAGCAGCTGCTTTGACTAACTTGGATCTTCATATAGAGTTAATGGTTATTCACTAAAAACT
GAGGCTAACTTGAAAGTTTTGAAGTCAATACCTAGTGAAAAATTAATGATTGAGACTCATGCACCTTGGTGTGGAGTCAA
AAGTACACATGCTAGATCAAAATATATAAAAACTACATTTCCTACCCAAAAAGAAGTGGGAAAATGGACATTGTTTAAGA
GATCAAAATGAACCCTGCCATTTAATTCAAATATTAAAGATAATGTCAGCAATAAGAGGTGAGAATCCCCTGGAGTTAGC
CAATACACTATATAACACCACCATTAAAATATTTTTTTCCTGACATG

Alignment

ORF - retro_tbel_707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.4 %
• Parental protein coverage: 77.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MFFSTVGCHPTRCDEFEKNNPDLYLMELLNLAENNKGKVVAIGECGLDFDRLQFCPKDIQLKYFEKQFEL
          MF.ST.GCHPTRCDE.EKNNPDLYLMELL.LAEN.K.KV.AIGE..LDFDR.Q.C.K..QLKYFE.QFEL
Retrocopy MFSSTAGCHPTRCDESEKNNPDLYLMELLDLAENSKRKVAAIGEYRLDFDRMQLCSKHTQLKYFENQFEL

Parental  SEQTKLPMFLHCRNSHAEFLDIMKRNRDR-CVGGVVHSFDGTKEAAAALIDLDLYIGF-NGCSLKTEANL
          SEQTKLPMFLHC.NSH.EFLDIMKRNRDR..V.GVVHSFDGTKE.AAAL..LDL.I...NG.SLKTEANL
Retrocopy SEQTKLPMFLHCGNSHDEFLDIMKRNRDR<VVAGVVHSFDGTKEVAAALTNLDLHIEL<NGYSLKTEANL

Parental  EVLKSIPSEKLMIETDAPWCGVKSTHAGSKYIKTTFPT-KKKWENGHCLRDRNEPCHIIQILEIMSAVRD
          .VLKSIPSEKLMIET.APWCGVKSTHA.SKYIKTTFPT.KKKWENGHCLRD.NEPCH.IQIL.IMSA.R.
Retrocopy KVLKSIPSEKLMIETHAPWCGVKSTHARSKYIKTTFPT>KKKWENGHCLRDQNEPCHLIQILKIMSAIRG

Parental  EDPLELANTLYNNTVKI-FFPDM
          E.PLELANTLYN.T.KI.FFPDM
Retrocopy ENPLELANTLYNTTIKI>FFPDM

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_707 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_707 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033446	1 retrocopy	retro_btau_463,
Homo sapiens	ENSG00000147687	1 retrocopy	retro_hsap_578,
Gorilla gorilla	ENSGGOG00000015875	1 retrocopy	retro_ggor_514,
Nomascus leucogenys	ENSNLEG00000005467	1 retrocopy	retro_nleu_804,
Oryctolagus cuniculus	ENSOCUG00000017403	1 retrocopy	retro_ocun_730,
Rattus norvegicus	ENSRNOG00000047198	1 retrocopy	retro_rnor_1737,
Tupaia belangeri	ENSTBEG00000006179	1 retrocopy	retro_tbel_707 ,