RetrogeneDB ID: retro_itri_62

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393313.1:405465..406005(+)
• Located in intron of: ENSSTOG00000000023

Retrocopy information

• Ensembl ID: ENSSTOG00000027953
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000016326
• Aliases: None
• Description: None

Sequence

>retro_itri_62
ATGGGAATTCTCTTCACCAGGATATGGAGACTGTTCAATCACCAGGAGCACAAAGTTATCATTGTTGGATTGGATAATGC
AGGAAAAACTACCATCCTTTACCAATTTTCAATGAATGAAGTTGTACATACATCCCCTACAATAGGAAGTAATGTAGAAG
AGATAGTGATTAATAATACACGTTTCCTAATGTGGGATATTGGTGGCCAAGAGTCTCTTCGTTCTTCCTGGAATACTTAT
TATACTAACACGGAGTTTGTAATAGTAGTTGTGGACAGTACAGACAGAGAGAGGATTTCTCTAACTAGAGAAGAACTCTA
CAAAATGTTAGCACATGAGGACCTAAGAAAAGCTGGATTACTGATTTTTGCTAATAAACAAGACGTTAAAGAATGCATGA
GTGTAGCAGAAATCTCCCAGTTTTTGAAGCTAACTTCTATTAAAGATCATCAGTGGCATATCCAGGCATGCTGTGCTCTT
ACTGGAGAGGGATTATGCCAAGGACTTGAATGGATGATGTCACGACTTAAGATTAGATGA

Alignment

ORF - retro_itri_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.04 %
• Parental protein coverage: 93.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFFISEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQESLRSSWNTY
          .F...EHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQESLRSSWNTY
Retrocopy LFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQESLRSSWNTY

Parental  YTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKECMSVAEISQFLKLTSIKDH
          YTNTEFVIVVVDSTDRERIS.TREELYKMLAHEDLRKAGLLIFANKQDVKECMSVAEISQFLKLTSIKDH
Retrocopy YTNTEFVIVVVDSTDRERISLTREELYKMLAHEDLRKAGLLIFANKQDVKECMSVAEISQFLKLTSIKDH

Parental  QWHIQACCALTGEGLCQGLEWMMSRLKIR
          QWHIQACCALTGEGLCQGLEWMMSRLKIR
Retrocopy QWHIQACCALTGEGLCQGLEWMMSRLKIR

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_62 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_62 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 26 parental genes, and 121 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005062	25 retrocopies	retro_chof_1109, retro_chof_1132, retro_chof_1205, retro_chof_1218, retro_chof_1407, retro_chof_1414, retro_chof_1443, retro_chof_1573, retro_chof_1712, retro_chof_1953, retro_chof_206, retro_chof_2081, retro_chof_2131, retro_chof_2142, retro_chof_2433, retro_chof_2464, retro_chof_2470, retro_chof_2713, retro_chof_373, retro_chof_547, retro_chof_836, retro_chof_857, retro_chof_865, retro_chof_972, retro_chof_98,
Callithrix jacchus	ENSCJAG00000003311	9 retrocopies	retro_cjac_1054, retro_cjac_1111, retro_cjac_1255, retro_cjac_1921, retro_cjac_2949, retro_cjac_3920, retro_cjac_4131, retro_cjac_4175, retro_cjac_4211,
Cavia porcellus	ENSCPOG00000005209	1 retrocopy	retro_cpor_913,
Dasypus novemcinctus	ENSDNOG00000013331	16 retrocopies	retro_dnov_105, retro_dnov_1165, retro_dnov_1244, retro_dnov_1953, retro_dnov_2159, retro_dnov_226, retro_dnov_2265, retro_dnov_2268, retro_dnov_2344, retro_dnov_2394, retro_dnov_563, retro_dnov_671, retro_dnov_713, retro_dnov_811, retro_dnov_818, retro_dnov_881,
Equus caballus	ENSECAG00000023672	1 retrocopy	retro_ecab_1087,
Erinaceus europaeus	ENSEEUG00000009350	3 retrocopies	retro_eeur_240, retro_eeur_642, retro_eeur_699,
Felis catus	ENSFCAG00000014742	2 retrocopies	retro_fcat_569, retro_fcat_65,
Homo sapiens	ENSG00000162980	5 retrocopies	retro_hsap_2549, retro_hsap_4715, retro_hsap_4768, retro_hsap_4894, retro_hsap_721,
Gorilla gorilla	ENSGGOG00000002066	5 retrocopies	retro_ggor_1131, retro_ggor_1594, retro_ggor_2930, retro_ggor_2971, retro_ggor_3056,
Loxodonta africana	ENSLAFG00000032104	4 retrocopies	retro_lafr_1178, retro_lafr_1228, retro_lafr_1244, retro_lafr_599,
Microcebus murinus	ENSMICG00000015788	7 retrocopies	retro_mmur_1271, retro_mmur_1487, retro_mmur_1586, retro_mmur_1618, retro_mmur_468, retro_mmur_652, retro_mmur_923,
Macaca mulatta	ENSMMUG00000010521	5 retrocopies	retro_mmul_2519, retro_mmul_2543, retro_mmul_2630, retro_mmul_616, retro_mmul_641,
Monodelphis domestica	ENSMODG00000003978	1 retrocopy	retro_mdom_75,
Mustela putorius furo	ENSMPUG00000000396	2 retrocopies	retro_mputfur_1477, retro_mputfur_352,
Mus musculus	ENSMUSG00000036093	1 retrocopy	retro_mmus_2232,
Nomascus leucogenys	ENSNLEG00000011191	2 retrocopies	retro_nleu_1259, retro_nleu_2280,
Otolemur garnettii	ENSOGAG00000011424	6 retrocopies	retro_ogar_1879, retro_ogar_2112, retro_ogar_2675, retro_ogar_3146, retro_ogar_3465, retro_ogar_728,
Pongo abelii	ENSPPYG00000012848	4 retrocopies	retro_pabe_3711, retro_pabe_3806, retro_pabe_3832, retro_pabe_621,
Pan troglodytes	ENSPTRG00000012538	5 retrocopies	retro_ptro_1486, retro_ptro_3134, retro_ptro_3175, retro_ptro_3262, retro_ptro_514,
Ictidomys tridecemlineatus	ENSSTOG00000011104	1 retrocopy	retro_itri_1390,
Ictidomys tridecemlineatus	ENSSTOG00000016022	2 retrocopies	retro_itri_1000, retro_itri_348,
Ictidomys tridecemlineatus	ENSSTOG00000016326	1 retrocopy	retro_itri_62 ,
Ictidomys tridecemlineatus	ENSSTOG00000027859	1 retrocopy	retro_itri_580,
Tupaia belangeri	ENSTBEG00000011511	8 retrocopies	retro_tbel_1173, retro_tbel_1540, retro_tbel_3202, retro_tbel_3464, retro_tbel_3681, retro_tbel_3835, retro_tbel_4207, retro_tbel_4665,
Tursiops truncatus	ENSTTRG00000015564	2 retrocopies	retro_ttru_1008, retro_ttru_1843,
Vicugna pacos	ENSVPAG00000002172	2 retrocopies	retro_vpac_318, retro_vpac_399,