RetrogeneDB ID: retro_itri_278

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:33502703..33502906(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD7
• Ensembl ID: ENSSTOG00000002724
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 7 [Source:HGNC Symbol;Acc:28314]

Sequence

>retro_itri_278
ATGCCTGAGGTGAAGTGGAAGCTGAGGGATTCTGACATTAAGTCCTTGCTTGCCAGAATCTAATACTCCTACCAAGTGTA
CAGATGAGAAAAACTATGACAGGGAAAGGTGTTCCACTGTCTTCTCAACATTTAAAAAACTACCCAAGATTCTGGAATTC
TGTCATGGGCCAGAAAAGACAGAATGGAGCGAAGCCATCTGTC

Alignment

ORF - retro_itri_278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.52 %
• Parental protein coverage: 78.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPVVTHRLRDPDI-NPCLLESDASRRCMDENNYDKERCSSYFLKYK-NCRRFWNSIMIQRRQNGVTPSM
          MP.V...LRD.DI..PCL.ES.....C.DE.NYD.ERCS..F...K.N..RFWNS.M.Q.RQNG..PS.
Retrocopy MPEVKWKLRDSDI>SPCLPESNTPTKCTDEKNYDRERCSTVFSTFK>NYPRFWNSVMGQKRQNGAKPSV

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_278 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_278 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007055	1 retrocopy	retro_cfam_1197,
Echinops telfairi	ENSETEG00000020301	2 retrocopies	retro_etel_1330, retro_etel_888,
Monodelphis domestica	ENSMODG00000024930	1 retrocopy	retro_mdom_1124,
Ictidomys tridecemlineatus	ENSSTOG00000002724	1 retrocopy	retro_itri_278 ,