RetrogeneDB ID:

retro_itri_479

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393294.1:13828952..13829530(+)
Located in intron of:ENSSTOG00000010061
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL15
Ensembl ID:ENSSTOG00000011153
Aliases:None
Description:ribosomal protein L15 [Source:HGNC Symbol;Acc:10306]


Retrocopy-Parental alignment summary:






>retro_itri_479
ATGGGCGCATACAAGTACACCCAGGAGCTATGAAGGAATAAGCAGCTGGATATATACACTTTCTTCTGAGGGTCCACTGC
CAGCAGTACTGCCAGCTTGCTGTGCTCCACAAGGCTCCCCACCCCACTCGGCTGGATAAAGTGCGCAGACTGGGATACAG
GGCTAAGCAAGTTTATGTCATATACAGGATCGTCTGTACCGTGGTGGCCGCAAACGCCCACTTCCTAAGGGTGCCACCTA
TAGCAAGCCTGTCCATCATGGCGTTAACTAGCTAAAGTTTGCCCGAAGTCTTCAGTCTGTTGCTGAGGATTGAGCTGGAC
ACTACTGTGGGTCTCTGAGAGTCCTGAATTCTTACTGGGTTGGTGAAGATTCCACATAGAAATTCTTCAAGGTTATCCTC
ATTGATCCATTCCACAAAGCTATTAGAACAAATCCCAACACTCAGTGAATCACCAAACTAGTCCACAAGCACAGGGAGAA
GCACAGCCTAACATGTGCAGGCCACAAGTTCCTTCCTATTGGTGGTTCTCGCGGGTGCAGCTTGGAGAAGATGCAATACT
CTCCAGCTACACCATTAC

ORF - retro_itri_479 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.13 %
Parental protein coverage: 100. %
Number of stop codons detected: 5
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMGAYKYIQELWRKKQSDV-MRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVIYRI-RVRR
MGAYKY.QEL.R.KQ.D....FLLRV.C.QY.QL..LH.AP.PTR.DK.RRLGY.AKQ.YVIYRI.R..R
RetrocopyMGAYKYTQEL*RNKQLDI<IHFLLRVHCQQYCQLAVLHKAPHPTRLDKVRRLGYRAKQVYVIYRI<RLYR
ParentalGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPF
GGRKRP.PKGATY.KPVHHGVN.LKFARSLQSVAE..AG..CG.LRVLNSYWVGEDST.KFF.VILIDPF
RetrocopyGGRKRPLPKGATYSKPVHHGVN*LKFARSLQSVAED*AGHYCGSLRVLNSYWVGEDST*KFFKVILIDPF
ParentalHKAIRRNPDTQWITKPVHKHRESRGLG-KGHKFHHTIGGSR-RAAWRRRNTLQLHRY
HKAIR.NP.TQ.ITK.VHKHRE...L...GHKF...IGGSR..AAWRR.NTLQLH.Y
RetrocopyHKAIRTNPNTQ*ITKLVHKHREKHSLTCAGHKF-LPIGGSR>GAAWRRCNTLQLHHY

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_479 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_479 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 16 parental genes, and 100 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000330802 retrocopies
retro_btau_152, retro_btau_201,
Cavia porcellus ENSCPOG000000022534 retrocopies
retro_cpor_620, retro_cpor_807, retro_cpor_900, retro_cpor_978,
Felis catus ENSFCAG000000262376 retrocopies
retro_fcat_1820, retro_fcat_285, retro_fcat_306, retro_fcat_610, retro_fcat_930, retro_fcat_985,
Gorilla gorilla ENSGGOG0000002427413 retrocopies
retro_ggor_1327, retro_ggor_1611, retro_ggor_1716, retro_ggor_1989, retro_ggor_2029, retro_ggor_2125, retro_ggor_2314, retro_ggor_2473, retro_ggor_39, retro_ggor_524, retro_ggor_552, retro_ggor_654, retro_ggor_771,
Myotis lucifugus ENSMLUG0000001380915 retrocopies
retro_mluc_1357, retro_mluc_1709, retro_mluc_1720, retro_mluc_2052, retro_mluc_2142, retro_mluc_2454, retro_mluc_425, retro_mluc_623, retro_mluc_701, retro_mluc_714, retro_mluc_748, retro_mluc_749, retro_mluc_907, retro_mluc_943, retro_mluc_99,
Macaca mulatta ENSMMUG000000063531 retrocopy
retro_mmul_209,
Monodelphis domestica ENSMODG000000148803 retrocopies
retro_mdom_1315, retro_mdom_1803, retro_mdom_918,
Mustela putorius furoENSMPUG000000121487 retrocopies
retro_mputfur_1011, retro_mputfur_1252, retro_mputfur_1291, retro_mputfur_314, retro_mputfur_346, retro_mputfur_658, retro_mputfur_669,
Mus musculus ENSMUSG000000124052 retrocopies
retro_mmus_118, retro_mmus_8,
Oryctolagus cuniculus ENSOCUG000000109612 retrocopies
retro_ocun_215, retro_ocun_228,
Otolemur garnettii ENSOGAG0000001305613 retrocopies
retro_ogar_1066, retro_ogar_1129, retro_ogar_1182, retro_ogar_1453, retro_ogar_1483, retro_ogar_1629, retro_ogar_1809, retro_ogar_2378, retro_ogar_270, retro_ogar_3058, retro_ogar_3096, retro_ogar_3349, retro_ogar_903,
Procavia capensis ENSPCAG000000119951 retrocopy
retro_pcap_265,
Rattus norvegicus ENSRNOG0000000814017 retrocopies
retro_rnor_1046, retro_rnor_1409, retro_rnor_1497, retro_rnor_1685, retro_rnor_1690, retro_rnor_1785, retro_rnor_2042, retro_rnor_2249, retro_rnor_2313, retro_rnor_2451, retro_rnor_2473, retro_rnor_2786, retro_rnor_2997, retro_rnor_428, retro_rnor_66, retro_rnor_710, retro_rnor_844,
Sus scrofa ENSSSCG000000280795 retrocopies
retro_sscr_1219, retro_sscr_1225, retro_sscr_448, retro_sscr_968, retro_sscr_997,
Ictidomys tridecemlineatus ENSSTOG00000011153 4 retrocopies
retro_itri_1445, retro_itri_1838, retro_itri_479 , retro_itri_785,
Tursiops truncatus ENSTTRG000000072445 retrocopies
retro_ttru_1305, retro_ttru_1358, retro_ttru_280, retro_ttru_920, retro_ttru_987,


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