RetrogeneDB ID: retro_itri_1452

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393493.1:292693..293116(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000014322
• Aliases: None
• Description: None

Sequence

>retro_itri_1452
CTTGGGAGTAAAATCTCTCGCAATTTCCAACTGTTGGAATAACAAGAAGAAGGCCAGAAAGGAGTAGGAGATGGCACAGT
TAGCTGGGGTCTAGAAGATGGCGAAGACATGACACTTATGAGATGGATAGGGATGATAATTGGGCCTCCAAGAACAATTT
ATGAAAACCGAATATACAGCCTTAAAATAGAATGTGGACCTAAATACCCAGAAGCATCCCTCTTTGTAAGATTTGTCACA
AAAATTAATATGAATGGAGTTAATAGTTCTAATGGAGTGGTGGACCCAAGAGCCATATCAGTGCTAGCAAAGTGGCAGAA
TTCATATAGCACCAAAGTTGTTCTTCAAGAGCTGCGGCACTTAATGATGTCTAAAGAAAATATGAAACTCCCTCAGCCTC
TGGAAGGACAGTGTTACAGCAAT

Alignment

ORF - retro_itri_1452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.07 %
• Parental protein coverage: 97.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTIYENRIYSLKIECGPKYP
          LG.K..RNF.LLE..EEGQKGVGDGTVSWGLED.EDMTL.RW.GMIIGPPRTIYENRIYSLKIECGPKYP
Retrocopy LGSKISRNFQLLE*QEEGQKGVGDGTVSWGLEDGEDMTLMRWIGMIIGPPRTIYENRIYSLKIECGPKYP

Parental  EAPPFVRFVTKINMNGVNSSNGVVDPRAISVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQCYS
          EA..FVRFVTKINMNGVNSSNGVVDPRAISVLAKWQNSYS.KVVLQELR.LMMSKENMKLPQP.EGQCYS
Retrocopy EASLFVRFVTKINMNGVNSSNGVVDPRAISVLAKWQNSYSTKVVLQELRHLMMSKENMKLPQPLEGQCYS

Parental  N
          N
Retrocopy N

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_1452 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1452 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 17 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027316	4 retrocopies	retro_btau_1196, retro_btau_1226, retro_btau_1307, retro_btau_415,
Canis familiaris	ENSCAFG00000032244	8 retrocopies	retro_cfam_1005, retro_cfam_1066, retro_cfam_1299, retro_cfam_1340, retro_cfam_1499, retro_cfam_2186, retro_cfam_494, retro_cfam_604,
Callithrix jacchus	ENSCJAG00000036984	10 retrocopies	retro_cjac_1076, retro_cjac_1952, retro_cjac_2810, retro_cjac_2865, retro_cjac_3081, retro_cjac_3140, retro_cjac_3258, retro_cjac_4089, retro_cjac_462, retro_cjac_974,
Equus caballus	ENSECAG00000011858	3 retrocopies	retro_ecab_1112, retro_ecab_250, retro_ecab_900,
Homo sapiens	ENSG00000244687	4 retrocopies	retro_hsap_2175, retro_hsap_2440, retro_hsap_2884, retro_hsap_4192,
Loxodonta africana	ENSLAFG00000027359	2 retrocopies	retro_lafr_1026, retro_lafr_1221,
Macaca mulatta	ENSMMUG00000012228	6 retrocopies	retro_mmul_1722, retro_mmul_2382, retro_mmul_351, retro_mmul_436, retro_mmul_629, retro_mmul_907,
Mustela putorius furo	ENSMPUG00000017557	3 retrocopies	retro_mputfur_1522, retro_mputfur_384, retro_mputfur_834,
Nomascus leucogenys	ENSNLEG00000006987	8 retrocopies	retro_nleu_1554, retro_nleu_1612, retro_nleu_1996, retro_nleu_2206, retro_nleu_2773, retro_nleu_3025, retro_nleu_304, retro_nleu_566,
Oryctolagus cuniculus	ENSOCUG00000026172	4 retrocopies	retro_ocun_1450, retro_ocun_1481, retro_ocun_454, retro_ocun_539,
Otolemur garnettii	ENSOGAG00000025894	12 retrocopies	retro_ogar_1381, retro_ogar_1391, retro_ogar_153, retro_ogar_1637, retro_ogar_1929, retro_ogar_2027, retro_ogar_2478, retro_ogar_2984, retro_ogar_3172, retro_ogar_3338, retro_ogar_620, retro_ogar_80,
Pan troglodytes	ENSPTRG00000013615	1 retrocopy	retro_ptro_64,
Rattus norvegicus	ENSRNOG00000025580	21 retrocopies	retro_rnor_1014, retro_rnor_1032, retro_rnor_1291, retro_rnor_1609, retro_rnor_1649, retro_rnor_1650, retro_rnor_1651, retro_rnor_2055, retro_rnor_2282, retro_rnor_2406, retro_rnor_2407, retro_rnor_2412, retro_rnor_2488, retro_rnor_2489, retro_rnor_2490, retro_rnor_2534, retro_rnor_2535, retro_rnor_2905, retro_rnor_819, retro_rnor_881, retro_rnor_991,
Sus scrofa	ENSSSCG00000030632	1 retrocopy	retro_sscr_431,
Ictidomys tridecemlineatus	ENSSTOG00000014322	6 retrocopies	retro_itri_1001, retro_itri_1002, retro_itri_1134, retro_itri_1452 , retro_itri_1600, retro_itri_992,
Ictidomys tridecemlineatus	ENSSTOG00000021769	2 retrocopies	retro_itri_568, retro_itri_900,
Tarsius syrichta	ENSTSYG00000002511	1 retrocopy	retro_tsyr_261,