RetrogeneDB ID: retro_tbel_88

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1082:276349..276930(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OLA1
• Ensembl ID: ENSTBEG00000007574
• Aliases: None
• Description: Obg-like ATPase 1 [Source:HGNC Symbol;Acc:28833]

Sequence

>retro_tbel_88
GTGGTTGTGAGAGGAGGAGATAAAAAACTAAAACCTCAATATGACATAATGTCCAAAGTCAAATCCTGGGTCATAGATCA
AAAGAAACCTATTCACTCGTATCATGATTGGAATGACAAAGAGATTAAAGTTTTGAATAAACACTTATTTTTTCACTTCA
AAATCAGGTCTACCTGGTTAATCTTTCTGGAAAAGACCACATTAGGAAGAAAAACAAATGCTTGATAAAAATTAAAGAGT
AGGTGGACAAGTATGGCCCACGTGCCTTGGTCATTCCTTTTAGTGGGGCCTTGGAACTCAAGTTGCAAGACTTAAATGCT
GAGGAGAGACAGAAGTATCTGGAAGCCAACATGACACAAAGGGCTTTGCCAAAGATCATTAAGGCTGGGCTTGCAGCACT
CCAAGTAGAATACTTCTTCACTGCGGGCCCAGATGAAGTACGAGCATGGACCATCAGGAAAGGGACCAAGTTTCCCCAGG
CTACAGGGAAGATTCACACAGATTTTGAAAAGGGATTCATCATGACTGAAGTAATGAAATACAAAGATTTTAAAGAGGAA
GTTTCTGAAAATGCGGTCAAG

Alignment

ORF - retro_tbel_88 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.13 %
• Parental protein coverage: 58.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAVRGGDKKLKPEYDIMCKVKSWVIDQKKPVRFYHDWNDKEIEVLNKHLFLTSK-PMVYLVNLSEKDYIR
          V.VRGGDKKLKP.YDIM.KVKSWVIDQKKP...YHDWNDKEI.VLNKHLF...K...VYLVNLS.KD.IR
Retrocopy VVVRGGDKKLKPQYDIMSKVKSWVIDQKKPIHSYHDWNDKEIKVLNKHLFFHFK<NQVYLVNLSGKDHIR

Parental  KKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAEERQKYLEANMTQSALPKIIKAGFAALQLEYF
          KKNK.LIKIKE.VDKY.P.ALVIPFSGALELKLQ.L.AEERQKYLEANMTQ.ALPKIIKAG.AALQ.EYF
Retrocopy KKNKCLIKIKE*VDKYGPRALVIPFSGALELKLQDLNAEERQKYLEANMTQRALPKIIKAGLAALQVEYF

Parental  FTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEVMKYEDFKEEGSENAVK
          FTAGPDEVRAWTIRKGTK.PQA.GKIHTDFEKGFIM.EVMKY.DFKEE.SENAVK
Retrocopy FTAGPDEVRAWTIRKGTKFPQATGKIHTDFEKGFIMTEVMKYKDFKEEVSENAVK

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_88 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_88 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 4 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000025196	1 retrocopy	retro_mluc_626,
Monodelphis domestica	ENSMODG00000009296	1 retrocopy	retro_mdom_1428,
Rattus norvegicus	ENSRNOG00000019047	1 retrocopy	retro_rnor_2219,
Tupaia belangeri	ENSTBEG00000007574	8 retrocopies	retro_tbel_1749, retro_tbel_2506, retro_tbel_3217, retro_tbel_3581, retro_tbel_418, retro_tbel_4356, retro_tbel_4475, retro_tbel_88 ,