RetrogeneDB ID: retro_itri_1350

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393449.1:1389368..1389620(+)
• Located in intron of: ENSSTOG00000012170

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC3
• Ensembl ID: ENSSTOG00000011979
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 3, 21kDa [Source:HGNC Symbol;Acc:706]

Sequence

>retro_itri_1350
AAAGATACAGATATTATGGATGAAGCCATCTGTTACTTCAAGGCCAATGCCTTCTTCAAGAACTATGAAATTAAGAATGA
AGCTGATAGGACCTTGATATATATCACCCTCTACATTTCTGAGTGTCTAAAGAAACTCCAAAAGTGCAATTCCAAAAGCC
AAGGTGAGAAAGAAATGTATACCCTGGGAATCACTAATTTTCCCATTCCTGGAGAGCCTGGTTTTCCACTTAATGCAATT
TATGCCAAACCT

Alignment

ORF - retro_itri_1350 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.43 %
• Parental protein coverage: 61.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIP
          KDTDI.DEAI.YFKAN.FFKNYEIKNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIP
Retrocopy KDTDIMDEAICYFKANAFFKNYEIKNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIP

Parental  GEPGFPLNAIYAKP
          GEPGFPLNAIYAKP
Retrocopy GEPGFPLNAIYAKP

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_1350 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1350 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008456	1 retrocopy	retro_cfam_11,
Callithrix jacchus	ENSCJAG00000009360	1 retrocopy	retro_cjac_242,
Echinops telfairi	ENSETEG00000006992	2 retrocopies	retro_etel_116, retro_etel_1323,
Felis catus	ENSFCAG00000004132	2 retrocopies	retro_fcat_1048, retro_fcat_73,
Monodelphis domestica	ENSMODG00000011628	1 retrocopy	retro_mdom_71,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252,
Oreochromis niloticus	ENSONIG00000003785	1 retrocopy	retro_onil_18,
Sorex araneus	ENSSARG00000000546	2 retrocopies	retro_sara_529, retro_sara_601,
Sarcophilus harrisii	ENSSHAG00000014805	3 retrocopies	retro_shar_144, retro_shar_439, retro_shar_576,
Ictidomys tridecemlineatus	ENSSTOG00000011979	1 retrocopy	retro_itri_1350 ,