RetrogeneDB ID: retro_itri_323

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:24101062..24101626(+)
• Located in intron of: ENSSTOG00000000121

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000012258
• Aliases: None
• Description: None

Sequence

>retro_itri_323
ATGGGAATCAACATACGCCACAAGAAGGACCGAAAGGTTCAGCGCAAGGAGCCCAAGAGCCAGGGCATCTACCTAGGGCT
GTTGGGCAAGTTGTACAGGTTTCTGGCTAAACGAACCAATTCTACCTTCAACCAAATGGTACTGAAGAGGTTGTTCATGA
GTCGCACCAATAGGCCACCTGTCTCCCTCCCTTGGATGATCCGGAAGATGAAGCTTCCTGGCCGAGAAAACAAAACAGCT
GTGGTCGTGGGGACCATGACGGATGATGTTTGTGTTCAGGAGGTGCCCAAACTGAAAGTGTGCGCACTGCGCGTGAGCAG
CCGAGCCCACAGCCGCATCCTCAAGGCTGGGGGCAAGATGCTCACCTTTGATCAACTGGCCCTGGACTCCCCCAAGGTCT
GTGGCACAGTCCTGCTCTTTGGTCCTCGCAAGGGCCAAGAGATGTACCGGCATTTTGGCAAGGCTCCTGGGATCCCACAC
AGCCACACCAAACCCTACGTCCACTCCAAGGGCAGGAAATTCGAGCAAGCCAGAGGCCAGAGAGCCAGCCATGCCTACAA
AAAC

Alignment

ORF - retro_itri_323 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPPLSLSRMIRKM
          MG..IRH.KDRKV.RKEPKSQ.IYL.LL.KLYRFLA.RTNSTFNQ.VLKRLFMSRTNRPP.SL..MIRKM
Retrocopy MGINIRHKKDRKVQRKEPKSQGIYLGLLGKLYRFLAKRTNSTFNQMVLKRLFMSRTNRPPVSLPWMIRKM

Parental  KLPGRENKTAVVVGTITDDVRVQEVPKLKVCALRVTSRARTRILKAGGKILTFDQLALDSPKGRGTVLLS
          KLPGRENKTAVVVGT.TDDV.VQEVPKLKVCALRV.SRA..RILKAGGK.LTFDQLALDSPK..GTVLL.
Retrocopy KLPGRENKTAVVVGTMTDDVCVQEVPKLKVCALRVSSRAHSRILKAGGKMLTFDQLALDSPKVCGTVLLF

Parental  GPRKGREVYRHFGKAPGTPHSHTKPYVRSKGRKFERARGRRASRGYKN
          GPRKG.E.YRHFGKAPG.PHSHTKPYV.SKGRKFE.ARG.RAS..YKN
Retrocopy GPRKGQEMYRHFGKAPGIPHSHTKPYVHSKGRKFEQARGQRASHAYKN

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_323 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_323 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 31 parental genes, and 195 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014872	3 retrocopies	retro_amel_1718, retro_amel_640, retro_amel_740,
Bos taurus	ENSBTAG00000015388	1 retrocopy	retro_btau_845,
Canis familiaris	ENSCAFG00000003967	7 retrocopies	retro_cfam_1285, retro_cfam_1383, retro_cfam_1507, retro_cfam_1853, retro_cfam_2044, retro_cfam_2199, retro_cfam_304,
Choloepus hoffmanni	ENSCHOG00000009140	6 retrocopies	retro_chof_1408, retro_chof_1668, retro_chof_1697, retro_chof_2025, retro_chof_427, retro_chof_436,
Callithrix jacchus	ENSCJAG00000000377	4 retrocopies	retro_cjac_1659, retro_cjac_2114, retro_cjac_2296, retro_cjac_529,
Cavia porcellus	ENSCPOG00000026334	4 retrocopies	retro_cpor_1062, retro_cpor_1322, retro_cpor_703, retro_cpor_733,
Equus caballus	ENSECAG00000021927	3 retrocopies	retro_ecab_478, retro_ecab_530, retro_ecab_880,
Erinaceus europaeus	ENSEEUG00000015872	5 retrocopies	retro_eeur_176, retro_eeur_299, retro_eeur_381, retro_eeur_419, retro_eeur_437,
Echinops telfairi	ENSETEG00000013157	6 retrocopies	retro_etel_1059, retro_etel_1211, retro_etel_1342, retro_etel_1373, retro_etel_1391, retro_etel_1715,
Felis catus	ENSFCAG00000008652	4 retrocopies	retro_fcat_1055, retro_fcat_1268, retro_fcat_1596, retro_fcat_718,
Homo sapiens	ENSG00000063177	11 retrocopies	retro_hsap_1073, retro_hsap_1202, retro_hsap_1331, retro_hsap_1617, retro_hsap_1706, retro_hsap_3235, retro_hsap_3794, retro_hsap_3895, retro_hsap_4001, retro_hsap_4111, retro_hsap_772,
Gorilla gorilla	ENSGGOG00000024878	7 retrocopies	retro_ggor_1038, retro_ggor_1280, retro_ggor_2200, retro_ggor_2550, retro_ggor_2624, retro_ggor_847, retro_ggor_937,
Loxodonta africana	ENSLAFG00000031267	1 retrocopy	retro_lafr_879,
Macropus eugenii	ENSMEUG00000000640	1 retrocopy	retro_meug_1568,
Myotis lucifugus	ENSMLUG00000009286	12 retrocopies	retro_mluc_1440, retro_mluc_1442, retro_mluc_1462, retro_mluc_1736, retro_mluc_1791, retro_mluc_1912, retro_mluc_2023, retro_mluc_480, retro_mluc_729, retro_mluc_786, retro_mluc_886, retro_mluc_904,
Macaca mulatta	ENSMMUG00000022158	3 retrocopies	retro_mmul_32, retro_mmul_55, retro_mmul_92,
Monodelphis domestica	ENSMODG00000014099	1 retrocopy	retro_mdom_906,
Mustela putorius furo	ENSMPUG00000003891	4 retrocopies	retro_mputfur_135, retro_mputfur_1410, retro_mputfur_529, retro_mputfur_974,
Mus musculus	ENSMUSG00000059070	11 retrocopies	retro_mmus_1655, retro_mmus_2025, retro_mmus_2091, retro_mmus_2303, retro_mmus_2462, retro_mmus_2622, retro_mmus_2790, retro_mmus_3424, retro_mmus_3621, retro_mmus_726, retro_mmus_740,
Nomascus leucogenys	ENSNLEG00000004537	11 retrocopies	retro_nleu_1124, retro_nleu_1136, retro_nleu_1410, retro_nleu_1799, retro_nleu_2006, retro_nleu_2380, retro_nleu_2464, retro_nleu_2597, retro_nleu_547, retro_nleu_577, retro_nleu_976,
Otolemur garnettii	ENSOGAG00000003562	16 retrocopies	retro_ogar_1167, retro_ogar_1474, retro_ogar_1563, retro_ogar_1753, retro_ogar_1978, retro_ogar_2394, retro_ogar_2419, retro_ogar_2527, retro_ogar_2613, retro_ogar_2833, retro_ogar_3319, retro_ogar_3456, retro_ogar_3458, retro_ogar_3459, retro_ogar_492, retro_ogar_996,
Oreochromis niloticus	ENSONIG00000006539	1 retrocopy	retro_onil_43,
Pongo abelii	ENSPPYG00000010206	6 retrocopies	retro_pabe_1003, retro_pabe_1337, retro_pabe_1402, retro_pabe_2681, retro_pabe_3100, retro_pabe_3176,
Pan troglodytes	ENSPTRG00000011245	10 retrocopies	retro_ptro_1084, retro_ptro_1155, retro_ptro_2187, retro_ptro_2574, retro_ptro_2649, retro_ptro_2790, retro_ptro_540, retro_ptro_730, retro_ptro_822, retro_ptro_908,
Pteropus vampyrus	ENSPVAG00000009524	10 retrocopies	retro_pvam_101, retro_pvam_1034, retro_pvam_1244, retro_pvam_1376, retro_pvam_1444, retro_pvam_427, retro_pvam_785, retro_pvam_883, retro_pvam_969, retro_pvam_990,
Rattus norvegicus	ENSRNOG00000021035	14 retrocopies	retro_rnor_1068, retro_rnor_1072, retro_rnor_1154, retro_rnor_1186, retro_rnor_1337, retro_rnor_1359, retro_rnor_2174, retro_rnor_2224, retro_rnor_2847, retro_rnor_2890, retro_rnor_516, retro_rnor_685, retro_rnor_856, retro_rnor_857,
Sarcophilus harrisii	ENSSHAG00000006564	2 retrocopies	retro_shar_571, retro_shar_659,
Sus scrofa	ENSSSCG00000025928	5 retrocopies	retro_sscr_1028, retro_sscr_118, retro_sscr_836, retro_sscr_864, retro_sscr_925,
Ictidomys tridecemlineatus	ENSSTOG00000012258	5 retrocopies	retro_itri_261, retro_itri_323 , retro_itri_828, retro_itri_853, retro_itri_957,
Tupaia belangeri	ENSTBEG00000001594	18 retrocopies	retro_tbel_1006, retro_tbel_126, retro_tbel_1591, retro_tbel_1599, retro_tbel_1600, retro_tbel_1719, retro_tbel_2618, retro_tbel_2628, retro_tbel_277, retro_tbel_2984, retro_tbel_3527, retro_tbel_3529, retro_tbel_3608, retro_tbel_3609, retro_tbel_4409, retro_tbel_4473, retro_tbel_4590, retro_tbel_737,
Tursiops truncatus	ENSTTRG00000008187	3 retrocopies	retro_ttru_1127, retro_ttru_1770, retro_ttru_42,