RetrogeneDB ID:

retro_itri_378

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393287.1:4342229..4343130(-)
Located in intron of:ENSSTOG00000013399
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSTOG00000005200
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_378
AGAATACAAAGGAAAGAGAAAAGGCAAAAATGTTGTGCATCAGCTCTCAGTAACATCAGAAGATTTATATAATGGTGCAC
AAGAAAACCGGCTCTGCAAAAGAATGTGATTTGTGACAAATGTGAAGGCTGAGGTGGTAAGAAAGGGGCAGTAGAGTGCT
GTCCCAAATGCCAAGGTACTGGAATGCAAATAAGAATTCATCAGTTAGAACCTGGAATGGTTCACCAAATTCAGTCTGTG
TACATGGAGAGCCCAGGTCAGCGGGAATGGATCAGTCCTAAAGATAGATGTAAAAGCTGCAATAGAAGGAAGATAGTTTG
AGAGAAGATGATTCTAGAAGTTAATATTGACAAAGGCATGAAAGATGGACTGAAGATAACATTCCAAGGTGAAGGAGACC
AAGAGCCAGAACTGGAACCAGGAGATATTATTGTTGTGTTAGATCAGAAGGCCCATGCTGTTTTTATTTGACAAGGAGAA
GGCCTCTTCATGTATATGGACATATAGCTGGTAGAAGCATTATGTGGCTTCCAGAAGCCAGTATCACTCTTTGATAATCG
AACTACAGTCATCACCTCTCATCCAGTCATATTGTCTAGCATGGAGATATAAAGTGTGTGCTAAATGAAGGTATGCCAAT
TTATCATAGACCAAATGAAAGGGTCACCTAACCATCGAGTTTAAGGTAAACTTTCCTGAAAATGGCTTTCTCCCTCCTGA
CAAACTTTCTTTGTTGGAAAAACTCCTATATCAGAGGAAGGAATTAGAAGAGACCGATGAAATGGATCTGGTAGAACTGA
TGGACTTTGATCCAAATCAGGAAGGATGACGCTATTATAATCGAGAAGCATATAAGGATGAAGAACATCAGCCCAGAGGT
GGTGTTCAGTGTCAAACCTCT

ORF - retro_itri_378 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.33 %
Parental protein coverage: 75.44 %
Number of stop codons detected: 6
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalRMQRE-RRGKNVVHQLSVTLEDLYNGA-TRKLALQKNVICDKCEGRGGKKGAVECCPNCRGTGMQIRIHQ
R.QR..R.GKNVVHQLSVT.EDLYNGA.TRK.ALQKNVICDKCEG.GGKKGAVECCP.C.GTGMQIRIHQ
RetrocopyRIQRK>RKGKNVVHQLSVTSEDLYNGA<TRKPALQKNVICDKCEG*GGKKGAVECCPKCQGTGMQIRIHQ
ParentalIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGMKDGQKITFHGEGDQEPGL
..PGMV.QIQSV.ME..G..E.ISPKDRCKSCN.RKIV.EK.ILEV.IDKGMKDG.KITF.GEGDQEP.L
RetrocopyLEPGMVHQIQSVYMESPGQREWISPKDRCKSCNRRKIV*EKMILEVNIDKGMKDGLKITFQGEGDQEPEL
ParentalEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTIVITSHP-GQIVKHGDIKCV
EPGDII.VLDQK.HAVF...GE.LFM.MDI.LVEALCGFQKP.S..DNRT.VITSHP...IV.HGDIKCV
RetrocopyEPGDIIVVLDQKAHAVFI*QGEGLFMYMDI*LVEALCGFQKPVSLFDNRTTVITSHP<SHIV*HGDIKCV
ParentalLNEGMPIYRRPYE-KGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERKEVEETDEMDQVELVDFDPNQER
LNEGMPIY.RP.E.KG.L.IEFKVNFPENGFL.PDKLSLLEKLL..RKE.EETDEMD.VEL.DFDPNQE.
RetrocopyLNEGMPIYHRPNE<KGHLTIEFKVNFPENGFLPPDKLSLLEKLLYQRKELEETDEMDLVELMDFDPNQEG
ParentalRRHYNGEAYEDDEHHPRGGVQCQTS
.R.YN.EAY.D.EH.PRGGVQCQTS
Retrocopy*RYYNREAYKDEEHQPRGGVQCQTS

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_378 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_378 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 25 parental genes, and 141 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000075894 retrocopies
retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Bos taurus ENSBTAG000000162656 retrocopies
retro_btau_1440, retro_btau_1599, retro_btau_1800, retro_btau_1826, retro_btau_574, retro_btau_828,
Canis familiaris ENSCAFG0000000181823 retrocopies
retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Choloepus hoffmanni ENSCHOG000000006319 retrocopies
retro_chof_1760, retro_chof_186, retro_chof_2020, retro_chof_2541, retro_chof_2694, retro_chof_287, retro_chof_417, retro_chof_498, retro_chof_946,
Callithrix jacchus ENSCJAG0000000802210 retrocopies
retro_cjac_1645, retro_cjac_1777, retro_cjac_2015, retro_cjac_2120, retro_cjac_2730, retro_cjac_2731, retro_cjac_2763, retro_cjac_3037, retro_cjac_3762, retro_cjac_887,
Cavia porcellus ENSCPOG000000004626 retrocopies
retro_cpor_1456, retro_cpor_225, retro_cpor_386, retro_cpor_396, retro_cpor_561, retro_cpor_781,
Dasypus novemcinctus ENSDNOG000000183423 retrocopies
retro_dnov_1139, retro_dnov_640, retro_dnov_884,
Homo sapiens ENSG000000860614 retrocopies
retro_hsap_2331, retro_hsap_2569, retro_hsap_3647, retro_hsap_4889,
Gorilla gorilla ENSGGOG000000070303 retrocopies
retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Myotis lucifugus ENSMLUG000000160867 retrocopies
retro_mluc_1245, retro_mluc_1485, retro_mluc_1737, retro_mluc_1878, retro_mluc_2062, retro_mluc_2579, retro_mluc_576,
Monodelphis domestica ENSMODG000000033847 retrocopies
retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mus musculus ENSMUSG000000284103 retrocopies
retro_mmus_2561, retro_mmus_2982, retro_mmus_3507,
Procavia capensis ENSPCAG000000122732 retrocopies
retro_pcap_184, retro_pcap_220,
Pongo abelii ENSPPYG000000191414 retrocopies
retro_pabe_1892, retro_pabe_2111, retro_pabe_2559, retro_pabe_2994,
Pan troglodytes ENSPTRG000000208524 retrocopies
retro_ptro_1499, retro_ptro_1705, retro_ptro_177, retro_ptro_2472,
Pteropus vampyrus ENSPVAG000000114701 retrocopy
retro_pvam_672,
Rattus norvegicus ENSRNOG000000070292 retrocopies
retro_rnor_2208, retro_rnor_608,
Sorex araneus ENSSARG000000013735 retrocopies
retro_sara_280, retro_sara_312, retro_sara_671, retro_sara_741, retro_sara_748,
Sarcophilus harrisii ENSSHAG000000123661 retrocopy
retro_shar_762,
Ictidomys tridecemlineatus ENSSTOG000000040071 retrocopy
retro_itri_343,
Ictidomys tridecemlineatus ENSSTOG00000005200 4 retrocopies
retro_itri_265, retro_itri_303, retro_itri_378 , retro_itri_809,
Ictidomys tridecemlineatus ENSSTOG000000094491 retrocopy
retro_itri_1356,
Tupaia belangeri ENSTBEG0000000059623 retrocopies
retro_tbel_1281, retro_tbel_134, retro_tbel_1529, retro_tbel_1542, retro_tbel_2260, retro_tbel_2293, retro_tbel_2316, retro_tbel_2428, retro_tbel_2445, retro_tbel_2917, retro_tbel_2965, retro_tbel_2972, retro_tbel_329, retro_tbel_3345, retro_tbel_3353, retro_tbel_3692, retro_tbel_4014, retro_tbel_4223, retro_tbel_432, retro_tbel_591, retro_tbel_617, retro_tbel_634, retro_tbel_842,
Tarsius syrichta ENSTSYG000000013294 retrocopies
retro_tsyr_110, retro_tsyr_1384, retro_tsyr_1921, retro_tsyr_57,
Tursiops truncatus ENSTTRG000000073874 retrocopies
retro_ttru_1181, retro_ttru_1551, retro_ttru_567, retro_ttru_783,


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