RetrogeneDB ID: retro_shar_735

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861653.1:1297204..1297425(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRABP2
• Ensembl ID: ENSSHAG00000015843
• Aliases: None
• Description: cellular retinoic acid binding protein 2 [Source:HGNC Symbol;Acc:2339]

Sequence

>retro_shar_735
GACTTCAAAATTGGGGAAGAGTTTGAGGAGCAGAGACTGGACGGGAGGCCCCATAAGAGCTTGGTGAAATGGGAAAGTCA
GAACAAGATGGTCTGTGAACAGAGATTCCTGAAAGGGGAGGCACCCAAGACCTCCTGGTCCCAGGAACTGGCCAGTGATG
AAGAATTGATCCTAAGCTAACAGCAGATGATGTAGTGTGCACCAGGGTCTATGTCAGGGAA

Alignment

ORF - retro_shar_735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.33 %
• Parental protein coverage: 53.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NFKIGEEFEEQTVDGRPCKSLVKWESQNKMVCEQRLLKGEGPKTSWSRELTNDGELILT-MTADDVVCTR
          .FKIGEEFEEQ..DGRP.KSLVKWESQNKMVCEQR.LKGE.PKTSWS.EL..D.ELIL...TADDVVCTR
Retrocopy DFKIGEEFEEQRLDGRPHKSLVKWESQNKMVCEQRFLKGEAPKTSWSQELASDEELILS<LTADDVVCTR

Parental  VYIRE
          VY.RE
Retrocopy VYVRE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_735 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000002295	1 retrocopy	retro_mmul_1110,
Sarcophilus harrisii	ENSSHAG00000003313	1 retrocopy	retro_shar_521,
Sarcophilus harrisii	ENSSHAG00000015843	1 retrocopy	retro_shar_735 ,
Vicugna pacos	ENSVPAG00000005002	1 retrocopy	retro_vpac_645,