RetrogeneDB ID: retro_itri_1152

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393388.1:2836010..2836247(+)
• Located in intron of: ENSSTOG00000010265

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3BGRL
• Ensembl ID: ENSSTOG00000013216
• Aliases: None
• Description: SH3 domain binding glutamic acid-rich protein like [Source:HGNC Symbol;Acc:10823]

Sequence

>retro_itri_1152
CAGAAAAAGATCCTGTAGCCAGTGAAGAGTCAGAAGCGGATGAGAGAAAATGCACCTGAAAATAGTGGACCCGCCACAGG
GTCCTCCCTGCCACCTCAGATTTTCAATGACAGCCAGAATTGTGGGGGCTAGGATGACTTTTTGGAAGCCCAAGAAAAGA
ACACAGTGTATGCCTTTTTAGGCTTGATGGCACCACCTGGTTTAAAGGAAGCAGAAGGCCAGGCACAGCAGCAAGCA

Alignment

ORF - retro_itri_1152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.56 %
• Parental protein coverage: 69.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKDIAANEENRKWMRENVPENSRPATGYPLPPQIFNESQYRGDYDAFFEARENNAVYAFLGLTAPPGSKE
          .K.I.......K.MREN.PENS.PATG..LPPQIFN.SQ..G..D.F.EA.E.N.VYAFLGL.APPG.KE
Retrocopy QKKIL*PVKSQKRMRENAPENSGPATGSSLPPQIFNDSQNCGG*DDFLEAQEKNTVYAFLGLMAPPGLKE

Parental  AEAQAKQQA
          AE.QA.QQA
Retrocopy AEGQAQQQA

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_1152 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1152 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004130	1 retrocopy	retro_chof_647,
Callithrix jacchus	ENSCJAG00000003568	2 retrocopies	retro_cjac_1102, retro_cjac_140,
Cavia porcellus	ENSCPOG00000012267	3 retrocopies	retro_cpor_1172, retro_cpor_244, retro_cpor_844,
Equus caballus	ENSECAG00000012612	1 retrocopy	retro_ecab_648,
Ictidomys tridecemlineatus	ENSSTOG00000013216	1 retrocopy	retro_itri_1152 ,