RetrogeneDB ID: retro_itri_340

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:27660696..27660889(-)
• Located in intron of: ENSSTOG00000005415

Retrocopy information

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

Parental gene information

• Parental gene symbol: NENF
• Ensembl ID: ENSSTOG00000022293
• Aliases: None
• Description: neudesin neurotrophic factor [Source:HGNC Symbol;Acc:30384]

Sequence

>retro_itri_340
GAAGATATGCATATCTACATGTCAGTGAAGGGAGTGATATTTGATCTCACCTCCAGAAATGAATTTTATGGGAGAGGGGC
TCCGTATAATACCTTGACTGGGAAGGTCTACCAGAGGGGTAGCCAAGATGTCCCTGGTTCCTATAGATCTCACCCATAAC
ACTACAATCCTTATAATCAGGGAGCTAGAGAGT

Alignment

ORF - retro_itri_340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.7 %
• Parental protein coverage: 57.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDQPIYLAVKGVVFDVTSGKEFYGRGAPYNALT-GKDSTRGVAKMSLDPADLTHDITGLTAKELES
          ED..IY..VKGV.FD.TS..EFYGRGAPYN.LT.G..STRGVAKMSL.P.DLTH..T.L...ELES
Retrocopy EDMHIYMSVKGVIFDLTSRNEFYGRGAPYNTLT>GR-STRGVAKMSLVPIDLTHNTTILIIRELES

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_340 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_340 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001341	1 retrocopy	retro_amel_836,
Bos taurus	ENSBTAG00000000759	1 retrocopy	retro_btau_1238,
Dasypus novemcinctus	ENSDNOG00000003399	1 retrocopy	retro_dnov_1256,
Felis catus	ENSFCAG00000031796	1 retrocopy	retro_fcat_1171,
Homo sapiens	ENSG00000117691	2 retrocopies	retro_hsap_3288, retro_hsap_379,
Gorilla gorilla	ENSGGOG00000025197	1 retrocopy	retro_ggor_830,
Macaca mulatta	ENSMMUG00000002142	2 retrocopies	retro_mmul_2064, retro_mmul_490,
Mus musculus	ENSMUSG00000037499	1 retrocopy	retro_mmus_3309,
Nomascus leucogenys	ENSNLEG00000002893	1 retrocopy	retro_nleu_1354,
Ochotona princeps	ENSOPRG00000014204	2 retrocopies	retro_opri_127, retro_opri_775,
Pongo abelii	ENSPPYG00000000236	2 retrocopies	retro_pabe_2717, retro_pabe_328,
Pan troglodytes	ENSPTRG00000001961	2 retrocopies	retro_ptro_2224, retro_ptro_295,
Sus scrofa	ENSSSCG00000015597	1 retrocopy	retro_sscr_393,
Ictidomys tridecemlineatus	ENSSTOG00000022293	2 retrocopies	retro_itri_1876, retro_itri_340 ,
Tarsius syrichta	ENSTSYG00000001880	3 retrocopies	retro_tsyr_1189, retro_tsyr_411, retro_tsyr_549,