RetrogeneDB ID: retro_itri_519

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393298.1:6484903..6485212(+)
• Located in intron of: ENSSTOG00000003254

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000006377
• Aliases: None
• Description: None

Sequence

>retro_itri_519
TTTGAGTCATTCTTGCTCTTCACCATTAACAAGGACACTAAGGTGCCCAATGCCTGTTTGTTCACCATCAACAAAGAAGA
CCACACACTAGGAAAAAAATCACAGCTGCTGAAGGATCCACAAGTGCTGTTTGCCAGCTACAAAGTCCCCTACCTCTTGG
AGCACAAGATCATCATCCGTGTGCAGACCAGCCAGGCCTATAGCCTGTAGGAGGCCTTTACCAACACCATCACAGACCTC
ATCAGTGAGCTCTCCTTGCTGGAAGAGTGGTTCAGGGTGGCCATTAAAGACTAGCAAGAAGGGATTGAA

Alignment

ORF - retro_itri_519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.9 %
• Parental protein coverage: 89.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQTTPDYS
          FE.....TINKDTKVPNACLFTINKEDHTLG...KSQLLKDPQVLFA.YKVP..LEHKIIIRVQT...YS
Retrocopy FESFLLFTINKDTKVPNACLFTINKEDHTLGK--KSQLLKDPQVLFASYKVPYLLEHKIIIRVQTSQAYS

Parental  PQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE
          ..EAFTN.ITDLISELSLLEE.FRVAIKD.QEGIE
Retrocopy L*EAFTNTITDLISELSLLEEWFRVAIKD*QEGIE

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_519 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_519 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
Loxodonta africana	ENSLAFG00000021507	1 retrocopy	retro_lafr_361,
Myotis lucifugus	ENSMLUG00000010467	2 retrocopies	retro_mluc_2479, retro_mluc_2499,
Sus scrofa	ENSSSCG00000024080	1 retrocopy	retro_sscr_53,
Ictidomys tridecemlineatus	ENSSTOG00000006377	1 retrocopy	retro_itri_519 ,