RetrogeneDB ID: retro_itri_251

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:33392605..33392787(+)
• Located in intron of: ENSSTOG00000022493

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN3
• Ensembl ID: ENSSTOG00000014353
• Aliases: None
• Description: high mobility group nucleosomal binding domain 3 [Source:HGNC Symbol;Acc:12312]

Sequence

>retro_itri_251
AGAGAAAACCTGCAGAAAATAGAAGGCAAAGATGGATCCAAAGTATCCAAACAGGAGGCCACGAGACAGTCTGCCAGGTC
GTCAGCAAACCTGCTCCACCAAAACCTGAACCTAAATCAAGAAAAGCACCTGCTAAGAAAGAACCTGGAACAAAGATTAG
CAGAGGTACAGGGGGAAAAAAA

Alignment

ORF - retro_itri_251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.81 %
• Parental protein coverage: 61.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKSPENSEGKDGSKVTKQEPTRRSARLSA-KPAPPKPEPKPRKASAKKEPGTKISRGAKGKK
          R......EGKDGSKV.KQE.TR.SAR.SA.KPAPPKPEPK.RKA.AKKEPGTKISRG..GKK
Retrocopy RENLQKIEGKDGSKVSKQEATRQSARSSA<KPAPPKPEPKSRKAPAKKEPGTKISRGTGGKK

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_251 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_251 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007015	1 retrocopy	retro_chof_2241,
Cavia porcellus	ENSCPOG00000012407	2 retrocopies	retro_cpor_1399, retro_cpor_147,
Felis catus	ENSFCAG00000028793	1 retrocopy	retro_fcat_1400,
Homo sapiens	ENSG00000118418	1 retrocopy	retro_hsap_231,
Gorilla gorilla	ENSGGOG00000006910	1 retrocopy	retro_ggor_293,
Macaca mulatta	ENSMMUG00000004351	1 retrocopy	retro_mmul_414,
Nomascus leucogenys	ENSNLEG00000012377	2 retrocopies	retro_nleu_68, retro_nleu_851,
Otolemur garnettii	ENSOGAG00000016487	1 retrocopy	retro_ogar_190,
Ochotona princeps	ENSOPRG00000009611	1 retrocopy	retro_opri_799,
Pan troglodytes	ENSPTRG00000018366	2 retrocopies	retro_ptro_1427, retro_ptro_200,
Ictidomys tridecemlineatus	ENSSTOG00000014353	1 retrocopy	retro_itri_251 ,
Tupaia belangeri	ENSTBEG00000015468	3 retrocopies	retro_tbel_1912, retro_tbel_4714, retro_tbel_615,
Tarsius syrichta	ENSTSYG00000005238	3 retrocopies	retro_tsyr_1569, retro_tsyr_268, retro_tsyr_976,