RetrogeneDB ID:

retro_itri_1664

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393619.1:154202..154673(+)
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:ENSSTOG00000020488
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_1664
ATGGCCAAGTCCAAGAAGCATATCACATTCAACCAGTCTCAAAAATGGTACAGAAATAGCATCAAGAAACCCCATCACAA
AGATATAAATCTCTTAAGTGGGTAGACCCCAAGTTCCTGAGAAATACGAGTTTTGCCAAACAGCACAAAAATCAGGGCCT
GAAAAACATGCAGGCAAAAAATGCCAAGGCAATGAGTGCAGGTGCTGAGGCATCAAGGCCCTGGTAAAGCCCAAAGAGGT
TAAGCCCAAGATGTGAAAGGGTGTGAACTGCAAACAAGATCGCCTTGTCTTCTTTGGCCTTCCAAGTTCAGGAAGCATGC
TTGTGCCCATGTGGCCAGGGATCATAGGCTCTGCCAGCCAAAGGCCAAAGCCCAAGCCCAATCCAAGACCCAGGCTGCAA
CTTCAGCTGCATGATCAGCTCCAGCTCTGACTCTGGCTCATGCTCCCAAAGATGCCCAGACTCCCAAGGGT

ORF - retro_itri_1664 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.87 %
Parental protein coverage: 95.18 %
Number of stop codons detected: 2
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMAKSKNHTTHNQSRKWHRNGIKKPR-SQRYESLKGVDPKFLRNMRFAKKHNKKGLKKMQANNAKAMSARA
MAKSK.H.T.NQS.KW.RN.IKKP..SQRY.SLK.VDPKFLRN..FAK.H...GLK.MQA.NAKAMSA.A
RetrocopyMAKSKKHITFNQSQKWYRNSIKKPH<SQRYKSLKWVDPKFLRNTSFAKQHKNQGLKNMQAKNAKAMSAGA
ParentalEA-IKALAKPKEVKPKMPKGASRKLDRLALLAHP-KHAKRARAHMARERRLSRPKAKAQA--KTQAATPA
EA.IKAL.KPKEVKPKM.KG...K.DRL.....P.K..K.A.AH.AR..RL..PKAKAQA..KTQAAT.A
RetrocopyEA<IKALVKPKEVKPKM*KGVNCKQDRLVFFGLP<KFRKHACAHVARDHRLCQPKAKAQAQSKTQAATSA
ParentalPASAPAPAAAPAPVPKGAQAPKG
..SAPA...A.A..PK.AQ.PKG
RetrocopyA*SAPALTLAHA--PKDAQTPKG

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_1664 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1664 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 27 parental genes, and 247 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091636 retrocopies
retro_amel_1373, retro_amel_1740, retro_amel_345, retro_amel_379, retro_amel_686, retro_amel_913,
Bos taurus ENSBTAG000000186281 retrocopy
retro_btau_982,
Callithrix jacchus ENSCJAG000000059519 retrocopies
retro_cjac_135, retro_cjac_160, retro_cjac_241, retro_cjac_29, retro_cjac_331, retro_cjac_348, retro_cjac_358, retro_cjac_73, retro_cjac_96,
Cavia porcellus ENSCPOG000000117381 retrocopy
retro_cpor_1509,
Dasypus novemcinctus ENSDNOG000000002097 retrocopies
retro_dnov_1743, retro_dnov_1900, retro_dnov_1923, retro_dnov_1952, retro_dnov_2050, retro_dnov_2163, retro_dnov_2614,
Equus caballus ENSECAG000000073972 retrocopies
retro_ecab_766, retro_ecab_904,
Felis catus ENSFCAG000000017629 retrocopies
retro_fcat_1032, retro_fcat_1132, retro_fcat_1753, retro_fcat_1774, retro_fcat_1897, retro_fcat_249, retro_fcat_485, retro_fcat_687, retro_fcat_952,
Homo sapiens ENSG0000016224423 retrocopies
retro_hsap_1098, retro_hsap_1146, retro_hsap_123, retro_hsap_1283, retro_hsap_1406, retro_hsap_1587, retro_hsap_170, retro_hsap_1759, retro_hsap_2053, retro_hsap_2358, retro_hsap_263, retro_hsap_2772, retro_hsap_2899, retro_hsap_3201, retro_hsap_3289, retro_hsap_3316, retro_hsap_3511, retro_hsap_3562, retro_hsap_3951, retro_hsap_3998, retro_hsap_4304, retro_hsap_863, retro_hsap_882,
Gorilla gorilla ENSGGOG0000002469116 retrocopies
retro_ggor_1007, retro_ggor_1090, retro_ggor_1205, retro_ggor_1315, retro_ggor_1330, retro_ggor_142, retro_ggor_1480, retro_ggor_1929, retro_ggor_224, retro_ggor_2247, retro_ggor_254, retro_ggor_2684, retro_ggor_312, retro_ggor_715, retro_ggor_863, retro_ggor_892,
Loxodonta africana ENSLAFG000000057575 retrocopies
retro_lafr_164, retro_lafr_184, retro_lafr_257, retro_lafr_461, retro_lafr_831,
Microcebus murinus ENSMICG000000027059 retrocopies
retro_mmur_192, retro_mmur_198, retro_mmur_303, retro_mmur_446, retro_mmur_508, retro_mmur_519, retro_mmur_657, retro_mmur_816, retro_mmur_938,
Myotis lucifugus ENSMLUG0000001508814 retrocopies
retro_mluc_1086, retro_mluc_1160, retro_mluc_134, retro_mluc_1377, retro_mluc_1699, retro_mluc_1955, retro_mluc_2228, retro_mluc_2522, retro_mluc_2523, retro_mluc_2575, retro_mluc_297, retro_mluc_421, retro_mluc_889, retro_mluc_915,
Macaca mulatta ENSMMUG000000192482 retrocopies
retro_mmul_1352, retro_mmul_218,
Monodelphis domestica ENSMODG0000002875017 retrocopies
retro_mdom_1013, retro_mdom_1187, retro_mdom_1201, retro_mdom_1328, retro_mdom_1445, retro_mdom_1452, retro_mdom_1505, retro_mdom_1532, retro_mdom_1604, retro_mdom_1665, retro_mdom_1904, retro_mdom_35, retro_mdom_504, retro_mdom_589, retro_mdom_612, retro_mdom_639, retro_mdom_995,
Mustela putorius furoENSMPUG000000117346 retrocopies
retro_mputfur_137, retro_mputfur_187, retro_mputfur_370, retro_mputfur_467, retro_mputfur_816, retro_mputfur_970,
Mus musculus ENSMUSG000000487583 retrocopies
retro_mmus_203, retro_mmus_231, retro_mmus_86,
Otolemur garnettii ENSOGAG000000137662 retrocopies
retro_ogar_290, retro_ogar_31,
Ochotona princeps ENSOPRG0000000882110 retrocopies
retro_opri_1166, retro_opri_277, retro_opri_373, retro_opri_535, retro_opri_607, retro_opri_69, retro_opri_700, retro_opri_877, retro_opri_983, retro_opri_99,
Procavia capensis ENSPCAG000000097124 retrocopies
retro_pcap_100, retro_pcap_101, retro_pcap_44, retro_pcap_97,
Pongo abelii ENSPPYG0000001381821 retrocopies
retro_pabe_1062, retro_pabe_1162, retro_pabe_1306, retro_pabe_1503, retro_pabe_1714, retro_pabe_1882, retro_pabe_2125, retro_pabe_2131, retro_pabe_2398, retro_pabe_2718, retro_pabe_2952, retro_pabe_3254, retro_pabe_3284, retro_pabe_3504, retro_pabe_3525, retro_pabe_404, retro_pabe_459, retro_pabe_491, retro_pabe_673, retro_pabe_687, retro_pabe_911,
Rattus norvegicus ENSRNOG0000001113815 retrocopies
retro_rnor_1045, retro_rnor_1158, retro_rnor_1161, retro_rnor_1422, retro_rnor_1702, retro_rnor_184, retro_rnor_1951, retro_rnor_2207, retro_rnor_2222, retro_rnor_2356, retro_rnor_2561, retro_rnor_338, retro_rnor_397, retro_rnor_63, retro_rnor_928,
Sorex araneus ENSSARG000000135728 retrocopies
retro_sara_108, retro_sara_309, retro_sara_329, retro_sara_347, retro_sara_400, retro_sara_53, retro_sara_637, retro_sara_669,
Sarcophilus harrisii ENSSHAG000000068542 retrocopies
retro_shar_355, retro_shar_444,
Sus scrofa ENSSSCG000000275737 retrocopies
retro_sscr_179, retro_sscr_182, retro_sscr_205, retro_sscr_206, retro_sscr_207, retro_sscr_208, retro_sscr_720,
Ictidomys tridecemlineatus ENSSTOG00000020488 14 retrocopies
retro_itri_1345, retro_itri_1433, retro_itri_1482, retro_itri_1586, retro_itri_1664 , retro_itri_1667, retro_itri_194, retro_itri_482, retro_itri_520, retro_itri_592, retro_itri_622, retro_itri_874, retro_itri_934, retro_itri_942,
Tursiops truncatus ENSTTRG000000035145 retrocopies
retro_ttru_1933, retro_ttru_213, retro_ttru_409, retro_ttru_449, retro_ttru_985,
Vicugna pacos ENSVPAG0000000128229 retrocopies
retro_vpac_102, retro_vpac_110, retro_vpac_120, retro_vpac_148, retro_vpac_155, retro_vpac_176, retro_vpac_188, retro_vpac_199, retro_vpac_243, retro_vpac_264, retro_vpac_28, retro_vpac_302, retro_vpac_305, retro_vpac_317, retro_vpac_325, retro_vpac_40, retro_vpac_401, retro_vpac_41, retro_vpac_416, retro_vpac_453, retro_vpac_462, retro_vpac_481, retro_vpac_547, retro_vpac_575, retro_vpac_58, retro_vpac_60, retro_vpac_602, retro_vpac_636, retro_vpac_98,


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