RetrogeneDB ID: retro_itri_27

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:4111783..4112377(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000022943
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004135
• Aliases: None
• Description: None

Sequence

>retro_itri_27
NAGACCTCCTTAGCTACGTGTTTTGCTCAAGAAACTTTTGGAAAACAGTACAAGCAAACTATAGGACTGGATTTCTTTTT
GAGAAGGATAACATTGCCAGGAAACTTGAATGTTACTCTTCAACTTTGGGATATAGGAGGACAGACAATAGGAGGAAAGA
TGTTGGATAAATATATCTATGGAGCACAGGGAATCCTCTTAGTATATGATATTACAAATTATCAAAGCTTTGAGAATTTA
GAAGATTGGTATACTGTGGTGAAGAAAGTGAGTGAAGAATCAGAAACTCAGCCGCTGGTTGCTTTGGTGGGCAATAAAAT
TGATTTGGAGCATATGCGAACAGTAAAACCTGAGAAACATTTACGATTTTGCCAGGAAAATGGTTTTAGTAGCCACTTTG
TCTCAGCCAAGACAGGAGACTCTGTCTTCCTGTGCTTCCAAAAAGTTGCTGCTGAAATCCTTGGGATAAAATTAAACAAA
GCAGAAATAGAACAGTCACAGAGGGTGGTGAAGGCAGATATTGTAAACTACAGCCAGGATTCCATGTCAAGAACTGTTCA
CCCGCCCCGGAGCTCCAAGTGTGCGGTGCAGTGA

Alignment

ORF - retro_itri_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.49 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLATCFAQETFGKQYKQTIGLDFFLRRITLPGNLNVTLQLWDIGGQTIGGKMLDKYIYGAQGILLVYDIT
          SLATCFAQETFGKQYKQTIGLDFFLRRITLPGNLNVTLQLWDIGGQTIGGKMLDKYIYGAQGILLVYDIT
Retrocopy SLATCFAQETFGKQYKQTIGLDFFLRRITLPGNLNVTLQLWDIGGQTIGGKMLDKYIYGAQGILLVYDIT

Parental  NYQSFENLEDWYTVVKKVSEESETQPLVALVGNKIDLEHMRTVKPEKHLRFCQENGFSSHFVSAKTGDSV
          NYQSFENLEDWYTVVKKVSEESETQPLVALVGNKIDLEHMRTVKPEKHLRFCQENGFSSHFVSAKTGDSV
Retrocopy NYQSFENLEDWYTVVKKVSEESETQPLVALVGNKIDLEHMRTVKPEKHLRFCQENGFSSHFVSAKTGDSV

Parental  FLCFQKVAAEILGIKLNKAEIEQSQRVVKADIVNYSQDSMSRTVHPPRSSMCAVQ
          FLCFQKVAAEILGIKLNKAEIEQSQRVVKADIVNYSQDSMSRTVHPPRSS.CAVQ
Retrocopy FLCFQKVAAEILGIKLNKAEIEQSQRVVKADIVNYSQDSMSRTVHPPRSSKCAVQ

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_27 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_27 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 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009344	1 retrocopy	retro_amel_469,
Choloepus hoffmanni	ENSCHOG00000001523	1 retrocopy	retro_chof_1365,
Callithrix jacchus	ENSCJAG00000012136	2 retrocopies	retro_cjac_2713, retro_cjac_4126,
Dasypus novemcinctus	ENSDNOG00000007750	4 retrocopies	retro_dnov_1426, retro_dnov_1771, retro_dnov_2419, retro_dnov_381,
Dipodomys ordii	ENSDORG00000012378	1 retrocopy	retro_dord_682,
Homo sapiens	ENSG00000157869	7 retrocopies	retro_hsap_4166, retro_hsap_4259, retro_hsap_4261, retro_hsap_4263, retro_hsap_4265, retro_hsap_4317, retro_hsap_4762,
Gorilla gorilla	ENSGGOG00000024190	1 retrocopy	retro_ggor_2966,
Macropus eugenii	ENSMEUG00000006792	4 retrocopies	retro_meug_1079, retro_meug_1182, retro_meug_1510, retro_meug_913,
Macaca mulatta	ENSMMUG00000022025	1 retrocopy	retro_mmul_1172,
Nomascus leucogenys	ENSNLEG00000016243	1 retrocopy	retro_nleu_2292,
Pongo abelii	ENSPPYG00000014610	1 retrocopy	retro_pabe_3707,
Pan troglodytes	ENSPTRG00000015920	2 retrocopies	retro_ptro_2893, retro_ptro_3171,
Rattus norvegicus	ENSRNOG00000017074	1 retrocopy	retro_rnor_1075,
Sarcophilus harrisii	ENSSHAG00000009274	1 retrocopy	retro_shar_602,
Sus scrofa	ENSSSCG00000022358	2 retrocopies	retro_sscr_482, retro_sscr_514,
Ictidomys tridecemlineatus	ENSSTOG00000004135	1 retrocopy	retro_itri_27 ,
Tarsius syrichta	ENSTSYG00000010939	2 retrocopies	retro_tsyr_1450, retro_tsyr_1750,
Tursiops truncatus	ENSTTRG00000003622	1 retrocopy	retro_ttru_697,