RetrogeneDB ID: retro_itri_256

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:3430785..3431078(-)
• Located in intron of: ENSSTOG00000015609

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS19
• Ensembl ID: ENSSTOG00000003502
• Aliases: None
• Description: ribosomal protein S19 [Source:HGNC Symbol;Acc:10402]

Sequence

>retro_itri_256
GGAGGCCACAGGATGCCTGGAGTTACTATGAAAGATGGAAACCAGAAGGAGTCTCTCAGAGCTCTGGCAGCTGTCCTCAA
CAAGTCCTGGAAGTTGAAAGTCTCCAAAGGGTAGATGAAGTCAAGCTGGCCAAAAACAAAGAGGTTGCTTCCTAAGAAGA
GAACCGCACACAAGCAGCTTTCACAGCATAGTACCTGTACCTCCAGGGTGGTGCTGCAGTTGGCTCCATGACCAAGATCT
ATGGGGGACCTTAGAGAGACGAGGTCATGCCCAGCCACTTCAGCTAAGGCTCT

Alignment

ORF - retro_itri_256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.34 %
• Parental protein coverage: 66.23 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGRTMPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEW-VDTVKLAKHKELAPYDENWFYTRAASTARHLY
          GG..MPGVT.KD.NQ.E..RALAA.L.KS.KLKV....VD.VKLAK.KE.A...EN...T.AA.TA..LY
Retrocopy GGHRMPGVTMKDGNQKESLRALAAVLNKSWKLKVSKG<VDEVKLAKNKEVAS*EEN--RTQAAFTA*YLY

Parental  LRGGAGVGSMTKIYGGRQRNGVMPSHFSRGS
          L.GGA.VGSMTKIYGG..R..VMPSHFS.GS
Retrocopy LQGGAAVGSMTKIYGGP*RDEVMPSHFS*GS

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_256 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_256 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 14 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028485	10 retrocopies	retro_cfam_1017, retro_cfam_1074, retro_cfam_1155, retro_cfam_1251, retro_cfam_1377, retro_cfam_149, retro_cfam_1998, retro_cfam_2212, retro_cfam_249, retro_cfam_499,
Callithrix jacchus	ENSCJAG00000020243	5 retrocopies	retro_cjac_1968, retro_cjac_2004, retro_cjac_2094, retro_cjac_2324, retro_cjac_3,
Dasypus novemcinctus	ENSDNOG00000002376	4 retrocopies	retro_dnov_1084, retro_dnov_1124, retro_dnov_1838, retro_dnov_2456,
Equus caballus	ENSECAG00000009738	2 retrocopies	retro_ecab_263, retro_ecab_815,
Homo sapiens	ENSG00000105372	5 retrocopies	retro_hsap_1400, retro_hsap_2417, retro_hsap_3174, retro_hsap_3642, retro_hsap_667,
Microcebus murinus	ENSMICG00000004554	1 retrocopy	retro_mmur_1480,
Macaca mulatta	ENSMMUG00000013429	8 retrocopies	retro_mmul_1201, retro_mmul_1358, retro_mmul_1807, retro_mmul_2007, retro_mmul_2443, retro_mmul_404, retro_mmul_607, retro_mmul_691,
Monodelphis domestica	ENSMODG00000010067	3 retrocopies	retro_mdom_1531, retro_mdom_1888, retro_mdom_883,
Mustela putorius furo	ENSMPUG00000007164	4 retrocopies	retro_mputfur_1071, retro_mputfur_1148, retro_mputfur_1470, retro_mputfur_1503,
Mus musculus	ENSMUSG00000040952	15 retrocopies	retro_mmus_1206, retro_mmus_1207, retro_mmus_1528, retro_mmus_1711, retro_mmus_1713, retro_mmus_2095, retro_mmus_2295, retro_mmus_2535, retro_mmus_2850, retro_mmus_3337, retro_mmus_3499, retro_mmus_639, retro_mmus_643, retro_mmus_684, retro_mmus_899,
Otolemur garnettii	ENSOGAG00000026255	3 retrocopies	retro_ogar_1315, retro_ogar_1663, retro_ogar_2305,
Rattus norvegicus	ENSRNOG00000048199	3 retrocopies	retro_rnor_221, retro_rnor_299, retro_rnor_51,
Sus scrofa	ENSSSCG00000003042	3 retrocopies	retro_sscr_1064, retro_sscr_308, retro_sscr_58,
Ictidomys tridecemlineatus	ENSSTOG00000003502	3 retrocopies	retro_itri_256 , retro_itri_751, retro_itri_872,