RetrogeneDB ID: retro_itri_35

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393302.1:10625551..10625914(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023419
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000019378
• Aliases: None
• Description: None

Sequence

>retro_itri_35
ATGATGCCGTCTCGTACTAATCTGGCTACTGGAATCCCCAGTAGTAAAGTAAAATACTCAAGGCTCTCCAGCACAGATGA
TGGCTACATTGACCTTCAGTTTAAGAAAAGCCCTCCTAAGATCCCTTATAAGGCCATTGCACTTGCCACTGTGCTGTTTT
TGATTGGCGCCTTTCTCATTATCATAGGCTCCCTCCTGCTGTCAGGCTACATTAGCAAAGGGGGGGCAGACCGGGCCGTT
CCTGTCCTGATTATTGGCATTCTGGTGTTCCTGCCAGGATTTTACCATCTGCGCATCGCCTACTATGCGTCTAAAGGCTA
CCGGGGTTACTCCTATGATGACATTCCAGACTTTGATGACTAA

Alignment

ORF - retro_itri_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMPSRTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKSPPKIPYKAIALATVLFLIGAFLIIIGSLLLSGY
          MMPSRTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKSPPKIPYKAIALATVLFLIGAFLIIIGSLLLSGY
Retrocopy MMPSRTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKSPPKIPYKAIALATVLFLIGAFLIIIGSLLLSGY

Parental  ISKGGADRAVPVLIIGILVFLPGFYHLRIAYYASKGYRGYSYDDIPDFDD
          ISKGGADRAVPVLIIGILVFLPGFYHLRIAYYASKGYRGYSYDDIPDFDD
Retrocopy ISKGGADRAVPVLIIGILVFLPGFYHLRIAYYASKGYRGYSYDDIPDFDD

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_35 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_35 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 20 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009083	1 retrocopy	retro_amel_1818,
Bos taurus	ENSBTAG00000006063	2 retrocopies	retro_btau_1079, retro_btau_147,
Canis familiaris	ENSCAFG00000006039	1 retrocopy	retro_cfam_981,
Choloepus hoffmanni	ENSCHOG00000010231	12 retrocopies	retro_chof_1228, retro_chof_1463, retro_chof_1812, retro_chof_2199, retro_chof_2210, retro_chof_2400, retro_chof_253, retro_chof_2584, retro_chof_2661, retro_chof_397, retro_chof_884, retro_chof_996,
Callithrix jacchus	ENSCJAG00000021275	2 retrocopies	retro_cjac_3112, retro_cjac_4206,
Dasypus novemcinctus	ENSDNOG00000005724	5 retrocopies	retro_dnov_1004, retro_dnov_2377, retro_dnov_2534, retro_dnov_373, retro_dnov_803,
Erinaceus europaeus	ENSEEUG00000014992	1 retrocopy	retro_eeur_77,
Echinops telfairi	ENSETEG00000018264	2 retrocopies	retro_etel_1604, retro_etel_665,
Homo sapiens	ENSG00000089063	3 retrocopies	retro_hsap_4890, retro_hsap_550, retro_hsap_783,
Loxodonta africana	ENSLAFG00000006412	1 retrocopy	retro_lafr_1033,
Myotis lucifugus	ENSMLUG00000023089	2 retrocopies	retro_mluc_1504, retro_mluc_1759,
Macaca mulatta	ENSMMUG00000013258	4 retrocopies	retro_mmul_1187, retro_mmul_2386, retro_mmul_2626, retro_mmul_856,
Nomascus leucogenys	ENSNLEG00000007719	3 retrocopies	retro_nleu_1256, retro_nleu_199, retro_nleu_723,
Otolemur garnettii	ENSOGAG00000001386	2 retrocopies	retro_ogar_1700, retro_ogar_3108,
Ochotona princeps	ENSOPRG00000008611	1 retrocopy	retro_opri_502,
Pongo abelii	ENSPPYG00000010796	3 retrocopies	retro_pabe_3801, retro_pabe_507, retro_pabe_916,
Pan troglodytes	ENSPTRG00000013221	4 retrocopies	retro_ptro_3030, retro_ptro_3257, retro_ptro_3258, retro_ptro_413,
Pteropus vampyrus	ENSPVAG00000002863	1 retrocopy	retro_pvam_44,
Ictidomys tridecemlineatus	ENSSTOG00000019378	1 retrocopy	retro_itri_35 ,
Vicugna pacos	ENSVPAG00000007009	1 retrocopy	retro_vpac_212,