RetrogeneDB ID: retro_itri_1393

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393472.1:3530498..3531080(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BID
• Ensembl ID: ENSSTOG00000020169
• Aliases: None
• Description: BH3 interacting domain death agonist [Source:HGNC Symbol;Acc:1050]

Sequence

>retro_itri_1393
GACTCTGAGGTCAGCAATGGTTCAGACCTCAGGGATGAGTACATCACAAACTTGCTGGTGCTTGACTTCCTTCAAAGCTT
CTCTGACTGTAAGTTTCACCAAGAGCTGAGAACTCTGGGCCAGGAGCTACCTGTGCGAACTTACCTGGAGGAGGAACCTG
AAGATGAGCTGCAGACTGACGGCGACCGTGCCAGTCTCTTCATGGAAAGAATAGAGGCAGATTCTGAAAGTCAAGAAGAA
GTTATATAGAACATTGCCCGGCATTTTGCCCAAGTCGGGGATGAAATGGACCATAGCATCCAGTCAAAACTGGTGAATGA
ACTGGTGGCACATTTTATGAATGCTGGACTGTCAGAGAAAGACAGAAGCAACTGCCTGGACACCACCCTGAAAGCAGCAA
TGCAGACTTACCCTAAAGACATGGAGAACCAGAAGACCATGCTGATTATGACCATGCTATAGGCCCAAAAGGTGGCCAAT
CATACACCATCCTTACTCCATGATGTGTTTCATGCAACAGTCAACTTTATTAACCAGAACCTATTTGCCTACCTGCGGGA
CTTAGTCAGAAATGAGATGGAC

Alignment

ORF - retro_itri_1393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.69 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NSQVSNGSDLRNEYITNLLVLDFLQSFSDCKFHQELRTLGQELPVRTYLEGEREDELQTDGNRASLFMGR
          .S.VSNGSDLR.EYITNLLVLDFLQSFSDCKFHQELRTLGQELPVRTYLE.E.EDELQTDG.RASLFM.R
Retrocopy DSEVSNGSDLRDEYITNLLVLDFLQSFSDCKFHQELRTLGQELPVRTYLEEEPEDELQTDGDRASLFMER

Parental  IEADSESQEEVIQNIARHLAQVGDEMDRSIQPELVNELVARFMNAGLSEEDRSNCLDTTLKAAMQTYPKD
          IEADSESQEEVI.NIARH.AQVGDEMD.SIQ..LVNELVA.FMNAGLSE.DRSNCLDTTLKAAMQTYPKD
Retrocopy IEADSESQEEVI*NIARHFAQVGDEMDHSIQSKLVNELVAHFMNAGLSEKDRSNCLDTTLKAAMQTYPKD

Parental  MENEKTMLIMTMLLAKKVANHTPSLLHDVFRATVNFINQNLFTYVRDLVRNEMD
          MEN.KTMLIMTML.A.KVANHTPSLLHDVF.ATVNFINQNLF.Y.RDLVRNEMD
Retrocopy MENQKTMLIMTML*AQKVANHTPSLLHDVFHATVNFINQNLFAYLRDLVRNEMD

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_1393 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1393 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016168	1 retrocopy	retro_cfam_1219,
Felis catus	ENSFCAG00000011109	1 retrocopy	retro_fcat_1823,
Ictidomys tridecemlineatus	ENSSTOG00000020169	1 retrocopy	retro_itri_1393 ,