RetrogeneDB ID: retro_itri_1081

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393371.1:2902511..2902706(+)
• Located in intron of: ENSSTOG00000012050

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELOF1
• Ensembl ID: ENSSTOG00000003687
• Aliases: None
• Description: elongation factor 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28691]

Sequence

>retro_itri_1081
AAACTCCAAGAAGACACCCTGGAGACCAAGTTCACCTGACCCTTTGCAACCACTTAAGTTTCATGATGTTAAAATGGACC
ATGACCACAACACTGGAGTCATTTCTTTTATAGCATTCCCAGAGGAATTCTAGATGACATCACATGTCTGTCAGAATCAG
TGAATGTGTACATCAGTTGAATCGTAGTCTGTGAG

Alignment

ORF - retro_itri_1081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.07 %
• Parental protein coverage: 79.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKMTGTLETQFTCPF-CNHE-KSCDVKMDRARNTGVISCTVCLEEF-QTPITYLSEPVDVYSDWIDACE
          K....TLET.FT.PF.CNH..K..DVKMD...NTGVIS.....EEF....IT.LSE.V.VY...I..CE
Retrocopy KLQEDTLETKFT*PF<CNHL<KFHDVKMDHDHNTGVISFIAFPEEF<LDDITCLSESVNVYIS*IVVCE

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_1081 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1081 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000064	1 retrocopy	retro_amel_1495,
Cavia porcellus	ENSCPOG00000020359	1 retrocopy	retro_cpor_1091,
Felis catus	ENSFCAG00000004926	1 retrocopy	retro_fcat_699,
Loxodonta africana	ENSLAFG00000001534	2 retrocopies	retro_lafr_1217, retro_lafr_771,
Macropus eugenii	ENSMEUG00000012101	1 retrocopy	retro_meug_2078,
Otolemur garnettii	ENSOGAG00000026211	1 retrocopy	retro_ogar_2878,
Ictidomys tridecemlineatus	ENSSTOG00000003687	1 retrocopy	retro_itri_1081 ,
Tupaia belangeri	ENSTBEG00000004812	1 retrocopy	retro_tbel_2163,
Tursiops truncatus	ENSTTRG00000001807	1 retrocopy	retro_ttru_1611,