RetrogeneDB ID:

retro_itri_88

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393734.1:160475..161585(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000023265
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSTOG00000003165
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_88
ATGGATCCCCGCAAAGTGAGCGAGCTTCGGGCCTTCGTGAAAATGTGTAAGCAGGATCCGAGCATCCTGCACACCGAGGA
GATGCGCTTCCTGAGAGAGTGGGTGGAGAGCATGTGGGGTAAAGTACCACCTGCTACTCATAAACCTAAATCAGAAGAAA
ATACCAAGGAAGAAAAAACAGATAGCAAGAAATCGGAAGAAAACATTAAGAGAGATGAGCCATCAAGTGAGGAAAGTGAT
CTAGAAATTGATAATGAAGGTGTAATTGAACCAGACACTGATGCTCCTCAAGAAATGGGAGATGAAAATGCGGAAATAAC
CGAGGAGATGATGGATCATGCAAATGAAAAGAAAGGGGCTGCCATTGAAGCCCTGAATGATGGTGAACTACAGAAAGCCA
TTGACTTGTTCACAGATGCTATCAAGCTAAATCCTCTCTTGGCCATTCTGTATGCCAAGAGAGCCAGTGTCTTCATCAAA
TTACAGAAGCCAAATGCTGCCATTCGAGACTGTGACAGAGCCATTGAAATAAATCCTGATTCAGCTCAGCCTTACAAGTG
GCGAGGGAAAGCCCACAGACTTTTGGGACACTGGGAAGAAGCAGCCCATGATCTTGCTCTTGCCTGTAAACTGGATTATG
ATGATGATGCTAGTGCAATGCTGAAAGAAGTTCAACCACGGGCCCAGAAAATTGCTGAACATCGGAGAAAATATGAACGA
AAACGTGAAGAGCGAGAGATCAAAGAAAGAATAGAAAGAGTTAAGAAGGCTCGAGAAGAACATGAGAGAGCCCAGAGGGA
GGAAGAAGCCAGACGACAAGCAGTAGCTCAGTTTGGCTCTTTTCCAGGTGGCTTTCCTGGAGGAATGCCTGGTAATTTTC
CTGGAGGAATGCCTGGAATGGGAGGGGGCATGCCTGGAATGGCAGGAATGCCTGGGCTCAATGAAATTCTTAGTGATCCG
GAGGTTCTTGCAGCCATGCAGGATCCAAAAGTTATGGTGGCCTTCCAGGATGTGGCCCAGAACCCAGCAAATATGTCAAA
ATATCAAAGCAACCCAAAGGTTATGAATCTCATCAGTAAATTGTCAGCCAAATTTGGAGGTCAAGTGTAA

ORF - retro_itri_88 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.83 %
Parental protein coverage: 99.73 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDPRKVSELRAFVKMCKQDPSVLHTEEMRFLREWVESMGGKVPPATHKPKSEENTKEEKTDSKKSEENIK
MDPRKVSELRAFVKMCKQDPS.LHTEEMRFLREWVESM.GKVPPATHKPKSEENTKEEKTDSKKSEENIK
RetrocopyMDPRKVSELRAFVKMCKQDPSILHTEEMRFLREWVESMWGKVPPATHKPKSEENTKEEKTDSKKSEENIK
ParentalRDEPSSEESDLEIDNEGVIEPDTDAPQEMGDENAEITEEMMDQANEKKGAAIEALNDGELQKAIDLFTDA
RDEPSSEESDLEIDNEGVIEPDTDAPQEMGDENAEITEEMMD.ANEKKGAAIEALNDGELQKAIDLFTDA
RetrocopyRDEPSSEESDLEIDNEGVIEPDTDAPQEMGDENAEITEEMMDHANEKKGAAIEALNDGELQKAIDLFTDA
ParentalIKLNPRLAILYAKRASVFIKLQKPNAAIRDCDRAIEINPDSAQPYKWRGKAHRLLGHWEEAAHDLALACK
IKLNP.LAILYAKRASVFIKLQKPNAAIRDCDRAIEINPDSAQPYKWRGKAHRLLGHWEEAAHDLALACK
RetrocopyIKLNPLLAILYAKRASVFIKLQKPNAAIRDCDRAIEINPDSAQPYKWRGKAHRLLGHWEEAAHDLALACK
ParentalLDYDDDASAMLKEVQPRAQKIAEHRRKYERKREEREIKERIERVKKAREEHERAQREEEARRQAGAQFGS
LDYDDDASAMLKEVQPRAQKIAEHRRKYERKREEREIKERIERVKKAREEHERAQREEEARRQA.AQFGS
RetrocopyLDYDDDASAMLKEVQPRAQKIAEHRRKYERKREEREIKERIERVKKAREEHERAQREEEARRQAVAQFGS
ParentalFPGGFPGGMPGNFPGGMPGRGGGMTGMAGMPGLNEILSDPEVLAAMQDPEVMVAFQDVAQNPANMSKYQS
FPGGFPGGMPGNFPGGMPG.GGGM.GMAGMPGLNEILSDPEVLAAMQDP.VMVAFQDVAQNPANMSKYQS
RetrocopyFPGGFPGGMPGNFPGGMPGMGGGMPGMAGMPGLNEILSDPEVLAAMQDPKVMVAFQDVAQNPANMSKYQS
ParentalNPKVMNLISKLSAKFGGQ
NPKVMNLISKLSAKFGGQ
RetrocopyNPKVMNLISKLSAKFGGQ

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_88 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_88 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 26 parental genes, and 148 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000052271 retrocopy
retro_acar_2,
Ailuropoda melanoleuca ENSAMEG000000138801 retrocopy
retro_amel_135,
Bos taurus ENSBTAG000000062024 retrocopies
retro_btau_254, retro_btau_427, retro_btau_621, retro_btau_658,
Canis familiaris ENSCAFG0000000113914 retrocopies
retro_cfam_1029, retro_cfam_1101, retro_cfam_1122, retro_cfam_1239, retro_cfam_1467, retro_cfam_1830, retro_cfam_1950, retro_cfam_1958, retro_cfam_247, retro_cfam_262, retro_cfam_582, retro_cfam_808, retro_cfam_901, retro_cfam_969,
Choloepus hoffmanni ENSCHOG000000126761 retrocopy
retro_chof_2222,
Callithrix jacchus ENSCJAG0000000464411 retrocopies
retro_cjac_1843, retro_cjac_1953, retro_cjac_2177, retro_cjac_2275, retro_cjac_2789, retro_cjac_3123, retro_cjac_3570, retro_cjac_4019, retro_cjac_488, retro_cjac_640, retro_cjac_685,
Cavia porcellus ENSCPOG000000022904 retrocopies
retro_cpor_1394, retro_cpor_1477, retro_cpor_166, retro_cpor_961,
Felis catus ENSFCAG000000118472 retrocopies
retro_fcat_920, retro_fcat_987,
Homo sapiens ENSG0000010038016 retrocopies
retro_hsap_1055, retro_hsap_1203, retro_hsap_178, retro_hsap_201, retro_hsap_2078, retro_hsap_2189, retro_hsap_2853, retro_hsap_3206, retro_hsap_3907, retro_hsap_4009, retro_hsap_4876, retro_hsap_500, retro_hsap_619, retro_hsap_756, retro_hsap_812, retro_hsap_986,
Gorilla gorilla ENSGGOG0000002674716 retrocopies
retro_ggor_1600, retro_ggor_1734, retro_ggor_1791, retro_ggor_1975, retro_ggor_2177, retro_ggor_2634, retro_ggor_2692, retro_ggor_277, retro_ggor_3045, retro_ggor_629, retro_ggor_666, retro_ggor_749, retro_ggor_788, retro_ggor_832, retro_ggor_833, retro_ggor_938,
Microcebus murinus ENSMICG000000088752 retrocopies
retro_mmur_481, retro_mmur_954,
Myotis lucifugus ENSMLUG000000077642 retrocopies
retro_mluc_1088, retro_mluc_2021,
Macaca mulatta ENSMMUG000000191183 retrocopies
retro_mmul_1842, retro_mmul_402, retro_mmul_438,
Monodelphis domestica ENSMODG000000130422 retrocopies
retro_mdom_1087, retro_mdom_31,
Mustela putorius furoENSMPUG0000001643215 retrocopies
retro_mputfur_1640, retro_mputfur_211, retro_mputfur_212, retro_mputfur_233, retro_mputfur_272, retro_mputfur_282, retro_mputfur_289, retro_mputfur_343, retro_mputfur_373, retro_mputfur_379, retro_mputfur_402, retro_mputfur_450, retro_mputfur_506, retro_mputfur_605, retro_mputfur_778,
Mus musculus ENSMUSG000000224032 retrocopies
retro_mmus_2997, retro_mmus_651,
Nomascus leucogenys ENSNLEG0000001537817 retrocopies
retro_nleu_1142, retro_nleu_1155, retro_nleu_1606, retro_nleu_1852, retro_nleu_2075, retro_nleu_2088, retro_nleu_2376, retro_nleu_2404, retro_nleu_247, retro_nleu_2555, retro_nleu_2765, retro_nleu_3121, retro_nleu_3122, retro_nleu_319, retro_nleu_447, retro_nleu_552, retro_nleu_988,
Otolemur garnettii ENSOGAG000000169321 retrocopy
retro_ogar_224,
Pongo abelii ENSPPYG0000001185814 retrocopies
retro_pabe_1004, retro_pabe_2181, retro_pabe_2361, retro_pabe_2657, retro_pabe_2885, retro_pabe_3183, retro_pabe_3673, retro_pabe_3794, retro_pabe_437, retro_pabe_554, retro_pabe_727, retro_pabe_763, retro_pabe_798, retro_pabe_880,
Pelodiscus sinensis ENSPSIG000000045531 retrocopy
retro_psin_42,
Pteropus vampyrus ENSPVAG000000119082 retrocopies
retro_pvam_1104, retro_pvam_393,
Rattus norvegicus ENSRNOG000000190708 retrocopies
retro_rnor_1360, retro_rnor_1725, retro_rnor_1798, retro_rnor_1976, retro_rnor_2204, retro_rnor_2372, retro_rnor_2481, retro_rnor_2543,
Sarcophilus harrisii ENSSHAG000000003192 retrocopies
retro_shar_70, retro_shar_767,
Sus scrofa ENSSSCG000000000711 retrocopy
retro_sscr_428,
Ictidomys tridecemlineatus ENSSTOG00000003165 1 retrocopy
retro_itri_88 ,
Tursiops truncatus ENSTTRG000000115105 retrocopies
retro_ttru_1245, retro_ttru_1425, retro_ttru_1615, retro_ttru_385, retro_ttru_670,




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