RetrogeneDB ID:

retro_itri_1033

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393360.1:5303881..5304347(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSTOG00000023443
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_1033
GACATTTAGACTCAGTGCGCTTATCAAAAGCAGCTAACCATCTTTCAAAACAAGAAGGGGGTCTTGCTGGGAAAAACTGG
CAAGGAGACGCCTCTAAATACCACAATAATATTAGCCTGCACTTTAGGACACCCAAGGAGGCCATTGAGGACACCTACAT
TAATAAGAATGTCCCTTTACTGGTAACATTTTCATCCAAGGGCAGATTCTGTTTGGGTGTGGTGACCAAGATGAAGATGC
AGGCACCACTGTTATCCTCTGGGACTATTTCCATTACATGTGCAAGTACAGTTACTGGGAGAAGCACCACAAGAACATGT
CTGTGCACCTATCCCCCTGCTTCAGGTATGTCCAGATTGGTGATATTATCACATTGGTCAAGTGCGGGCCCCTTAACAAG
ATAGTGCACTGTAATGTGCTCAAGGTCATCAAGGCTGCTGGCACCAAGAAGCAATTCCAGAAGTTC

ORF - retro_itri_1033 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.75 %
Parental protein coverage: 99.36 %
Number of stop codons detected: 1
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalDLDTERAYQKQPTIFQNKKRVLLGETGKEK-LPRYYKNIGLGFKTPKEAIEGTYIDK-KCPFTGNVSIRG
D..T..AYQKQ.TIFQNKK.VLLG.TGKE.....Y..NI.L.F.TPKEAIE.TYI.K..CPFTGN..I.G
RetrocopyDI*TQCAYQKQLTIFQNKKGVLLGKTGKET<ASKYHNNISLHFRTPKEAIEDTYINK<ECPFTGNIFIQG
ParentalRILSG-VVTKMKMQR-TIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECRPLSKTV
.IL.G.VVTKMKMQ..T.VI..DY.HY..KY...EK.HKNMSVHLSPCFR.VQIGDI.T...C.PL.K.V
RetrocopyQILFG>VVTKMKMQA<TTVILWDYFHYMCKYSYWEKHHKNMSVHLSPCFRYVQIGDIITLVKCGPLNKIV
ParentalRFNVLKVTKAAGTKKQFQKF
..NVLKV.KAAGTKKQFQKF
RetrocopyHCNVLKVIKAAGTKKQFQKF

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_1033 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1033 was not experimentally validated.

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.
Parental genes homology:
Parental genes homology involve 32 parental genes, and 176 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001402013 retrocopies
retro_amel_1038, retro_amel_1071, retro_amel_1398, retro_amel_1406, retro_amel_1475, retro_amel_246, retro_amel_262, retro_amel_317, retro_amel_64, retro_amel_757, retro_amel_759, retro_amel_764, retro_amel_859,
Bos taurus ENSBTAG000000139245 retrocopies
retro_btau_1282, retro_btau_1369, retro_btau_1499, retro_btau_1529, retro_btau_888,
Canis familiaris ENSCAFG000000036319 retrocopies
retro_cfam_126, retro_cfam_1333, retro_cfam_1572, retro_cfam_1656, retro_cfam_1669, retro_cfam_1900, retro_cfam_1955, retro_cfam_2121, retro_cfam_248,
Callithrix jacchus ENSCJAG000000000691 retrocopy
retro_cjac_340,
Cavia porcellus ENSCPOG000000151451 retrocopy
retro_cpor_534,
Danio rerio ENSDARG000000530581 retrocopy
retro_drer_15,
Dasypus novemcinctus ENSDNOG000000161079 retrocopies
retro_dnov_1055, retro_dnov_1102, retro_dnov_1629, retro_dnov_1729, retro_dnov_188, retro_dnov_2520, retro_dnov_586, retro_dnov_68, retro_dnov_754,
Dipodomys ordii ENSDORG000000121951 retrocopy
retro_dord_635,
Equus caballus ENSECAG000000003701 retrocopy
retro_ecab_868,
Erinaceus europaeus ENSEEUG000000033921 retrocopy
retro_eeur_75,
Felis catus ENSFCAG0000000919613 retrocopies
retro_fcat_1362, retro_fcat_1491, retro_fcat_1535, retro_fcat_1564, retro_fcat_1719, retro_fcat_1945, retro_fcat_197, retro_fcat_1991, retro_fcat_273, retro_fcat_507, retro_fcat_792, retro_fcat_854, retro_fcat_995,
Homo sapiens ENSG000001425346 retrocopies
retro_hsap_1017, retro_hsap_1068, retro_hsap_230, retro_hsap_2449, retro_hsap_4242, retro_hsap_4674,
Gorilla gorilla ENSGGOG000000029366 retrocopies
retro_ggor_1525, retro_ggor_2843, retro_ggor_2900, retro_ggor_292, retro_ggor_805, retro_ggor_842,
Loxodonta africana ENSLAFG000000162172 retrocopies
retro_lafr_622, retro_lafr_658,
Macropus eugenii ENSMEUG000000086492 retrocopies
retro_meug_1176, retro_meug_1640,
Microcebus murinus ENSMICG000000025428 retrocopies
retro_mmur_1278, retro_mmur_1317, retro_mmur_186, retro_mmur_295, retro_mmur_430, retro_mmur_452, retro_mmur_812, retro_mmur_820,
Myotis lucifugus ENSMLUG000000304751 retrocopy
retro_mluc_539,
Macaca mulatta ENSMMUG000000075496 retrocopies
retro_mmul_1147, retro_mmul_1856, retro_mmul_2464, retro_mmul_413, retro_mmul_634, retro_mmul_813,
Monodelphis domestica ENSMODG000000134347 retrocopies
retro_mdom_1185, retro_mdom_1284, retro_mdom_1421, retro_mdom_1950, retro_mdom_636, retro_mdom_922, retro_mdom_978,
Mustela putorius furoENSMPUG0000000259910 retrocopies
retro_mputfur_1402, retro_mputfur_1507, retro_mputfur_200, retro_mputfur_306, retro_mputfur_345, retro_mputfur_485, retro_mputfur_491, retro_mputfur_626, retro_mputfur_781, retro_mputfur_897,
Mus musculus ENSMUSG0000000342916 retrocopies
retro_mmus_1738, retro_mmus_2230, retro_mmus_2255, retro_mmus_2322, retro_mmus_2486, retro_mmus_2854, retro_mmus_3048, retro_mmus_3051, retro_mmus_3060, retro_mmus_3342, retro_mmus_398, retro_mmus_404, retro_mmus_714, retro_mmus_754, retro_mmus_842, retro_mmus_860,
Otolemur garnettii ENSOGAG000000046277 retrocopies
retro_ogar_1290, retro_ogar_1813, retro_ogar_1910, retro_ogar_2037, retro_ogar_2573, retro_ogar_2640, retro_ogar_840,
Procavia capensis ENSPCAG000000041462 retrocopies
retro_pcap_333, retro_pcap_54,
Pongo abelii ENSPPYG000000258605 retrocopies
retro_pabe_1800, retro_pabe_3396, retro_pabe_3631, retro_pabe_855, retro_pabe_889,
Pelodiscus sinensis ENSPSIG000000110891 retrocopy
retro_psin_35,
Pan troglodytes ENSPTRG000000112991 retrocopy
retro_ptro_88,
Rattus norvegicus ENSRNOG0000002059518 retrocopies
retro_rnor_1132, retro_rnor_1159, retro_rnor_1261, retro_rnor_1299, retro_rnor_1363, retro_rnor_1414, retro_rnor_1435, retro_rnor_1451, retro_rnor_1635, retro_rnor_1790, retro_rnor_2000, retro_rnor_2647, retro_rnor_385, retro_rnor_394, retro_rnor_538, retro_rnor_737, retro_rnor_835, retro_rnor_989,
Sorex araneus ENSSARG000000032362 retrocopies
retro_sara_11, retro_sara_469,
Sarcophilus harrisii ENSSHAG000000049911 retrocopy
retro_shar_649,
Sus scrofa ENSSSCG000000031652 retrocopies
retro_sscr_432, retro_sscr_887,
Ictidomys tridecemlineatus ENSSTOG00000023443 2 retrocopies
retro_itri_1033 , retro_itri_805,
Tupaia belangeri ENSTBEG0000001667716 retrocopies
retro_tbel_125, retro_tbel_1361, retro_tbel_1753, retro_tbel_2071, retro_tbel_2207, retro_tbel_2808, retro_tbel_2947, retro_tbel_319, retro_tbel_3401, retro_tbel_3571, retro_tbel_3600, retro_tbel_3742, retro_tbel_449, retro_tbel_604, retro_tbel_801, retro_tbel_836,


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