RetrogeneDB ID: retro_itri_642

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393308.1:3453445..3453802(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COQ7
• Ensembl ID: ENSSTOG00000003901
• Aliases: None
• Description: coenzyme Q7 homolog, ubiquinone (yeast) [Source:HGNC Symbol;Acc:2244]

Sequence

>retro_itri_642
GCAGTTCCCTCCTTGTGGCATCTGCTCACCAGAGCCCAGGGGCCCCTCTCAGCTTGTGGAAGAATCAGTGTCAGGTTTCA
CAGTTCTGTAATGACCTTAGATAACATCAATTTTGTGGCCGTGGATTGAATAATCCTGCTGAATTATGCAGGTGAATATG
GGGCAAACCATATCCATGCAGGCCAGATGGCCATCCTGGGCAGGACAAGCATAGGGCTGGTCTTTTGGAAAATGTGGGAT
CAAGAAAAGAACCAGTTGAAAAAGTTTAGCAAGCTGATGAGTGCCTTCAGGGTCCGACCAAAAATTCTCATGCCCTTTTG
GAATGTGCTGGGCTTTGCACTGGGGGCAGGGGCCGCC

Alignment

ORF - retro_itri_642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.5 %
• Parental protein coverage: 55.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAPSLWRLRLGARRPLSACGSRVGTRARSSGMTLDNVNRAALDRIIRVDHAGEYGANRIYAGQMAVLGRT
          A.PSLW.L...A..PLSACG.R...R..SS.MTLDN.N..A.D.II....AGEYGAN.I.AGQMA.LGRT
Retrocopy AVPSLWHLLTRAQGPLSACG-RISVRFHSSVMTLDNINFVAVD*IILLNYAGEYGANHIHAGQMAILGRT

Parental  SVGPVIQKMWDQEKDHLKKFNELMVAFRVRPTVLMPFWNVVGFALGAGTA
          S.G.V..KMWDQEK..LKKF..LM.AFRVRP..LMPFWNV.GFALGAG.A
Retrocopy SIGLVFWKMWDQEKNQLKKFSKLMSAFRVRPKILMPFWNVLGFALGAGAA

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_642 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_642 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000406	4 retrocopies	retro_chof_1015, retro_chof_1791, retro_chof_291, retro_chof_569,
Echinops telfairi	ENSETEG00000016203	2 retrocopies	retro_etel_1424, retro_etel_1605,
Macaca mulatta	ENSMMUG00000006604	1 retrocopy	retro_mmul_347,
Sarcophilus harrisii	ENSSHAG00000018111	1 retrocopy	retro_shar_273,
Ictidomys tridecemlineatus	ENSSTOG00000003901	1 retrocopy	retro_itri_642 ,
Tupaia belangeri	ENSTBEG00000001643	1 retrocopy	retro_tbel_1265,