RetrogeneDB ID: retro_itri_142

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393430.1:2487316..2487787(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021298
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000027493
• Aliases: None
• Description: None

Sequence

>retro_itri_142
ATGTCTTCTGAAGAAGGGAAGCTGTTCGTGGGAGGACTCAACTTCAATACTGATGAGCAGGCGCTGGAAGACCACTTCAG
CAGCTTTGGGCCTATTTCTGAGGTGGTTGTTGTCAAGGACCGGGAGACTCAGCGATCCCGGGGTTTTGGCTTCATCACCT
TCACCAATCCAGAACATGCCTCAGATGCCATGAAAGCCATGAATGGAGAGTCCCTGGATGGTCGGCAGATCCGGGTGGAC
CATGCAGGCAAGTCTGCCCGGGGCACCAGAGGGGGTGCCTTTGGGGCCCATGGGCGTGGTCGCAGCTACTCTAGAGGTGG
TGGGGACCGGGGATATGGGAGTGGCCGGTATGACAGTCGACCTGGAGGTTATGGATATGGATACGGACGGTCCCGAGACT
ATAGTGGCAGAAGCCAGGGTGGCTATGACCGCTACTCAGGAGGAAATTATCGAGACAATTATGACAACTGA

Alignment

ORF - retro_itri_142 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.36 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASDAMKAMNGE
          MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASDAMKAMNGE
Retrocopy MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASDAMKAMNGE

Parental  SLDGRQIRVDHAGKSARGTRGGAFGAHGRGRSYSRGGGDQGYGSGRYDSRPGGYGYGYGRSRDYSGRSQG
          SLDGRQIRVDHAGKSARGTRGGAFGAHGRGRSYSRGGGD.GYGSGRYDSRPGGYGYGYGRSRDYSGRSQG
Retrocopy SLDGRQIRVDHAGKSARGTRGGAFGAHGRGRSYSRGGGDRGYGSGRYDSRPGGYGYGYGRSRDYSGRSQG

Parental  GYDRYSGGNYRDNYDN
          GYDRYSGGNYRDNYDN
Retrocopy GYDRYSGGNYRDNYDN

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_142 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_142 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.

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Ailuropoda melanoleuca	ENSAMEG00000012653	1 retrocopy	retro_amel_519,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Cavia porcellus	ENSCPOG00000003553	1 retrocopy	retro_cpor_950,
Dasypus novemcinctus	ENSDNOG00000010420	16 retrocopies	retro_dnov_1343, retro_dnov_1380, retro_dnov_1463, retro_dnov_151, retro_dnov_1718, retro_dnov_180, retro_dnov_2034, retro_dnov_2076, retro_dnov_212, retro_dnov_213, retro_dnov_2217, retro_dnov_2367, retro_dnov_2581, retro_dnov_733, retro_dnov_778, retro_dnov_974,
Dipodomys ordii	ENSDORG00000000182	1 retrocopy	retro_dord_547,
Equus caballus	ENSECAG00000024257	2 retrocopies	retro_ecab_130, retro_ecab_589,
Homo sapiens	ENSG00000102317	1 retrocopy	retro_hsap_265,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Myotis lucifugus	ENSMLUG00000003996	1 retrocopy	retro_mluc_1013,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Nomascus leucogenys	ENSNLEG00000007841	2 retrocopies	retro_nleu_2591, retro_nleu_867,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pan troglodytes	ENSPTRG00000021864	1 retrocopy	retro_ptro_222,
Pteropus vampyrus	ENSPVAG00000015630	1 retrocopy	retro_pvam_953,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Ictidomys tridecemlineatus	ENSSTOG00000006720	2 retrocopies	retro_itri_1807, retro_itri_776,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142 ,
Tarsius syrichta	ENSTSYG00000008670	4 retrocopies	retro_tsyr_1733, retro_tsyr_197, retro_tsyr_2002, retro_tsyr_679,
Tursiops truncatus	ENSTTRG00000008587	3 retrocopies	retro_ttru_1898, retro_ttru_928, retro_ttru_938,