RetrogeneDB ID:

retro_dord_656

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_48746:6812..7304(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Tmem126a
Ensembl ID:ENSDORG00000006408
Aliases:None
Description:transmembrane protein 126A [Source:MGI Symbol;Acc:MGI:1913521]


Retrocopy-Parental alignment summary:






>retro_dord_656
AATGTCCTTGAATATGGATCAACATACGTTGGACTTAACGCTGCTTTCTGTGGTCTAATAGATAATAGTCTTTTTCGACA
TGCCTTGCATGTTATAAAAGCGCCAGTGGCATCTGGCTTACCAATAGCAGTGATGCCATTTTTGACAGCTAATGTGGCTT
ACAAAGGTTTTGTAAGTTTACCTTTGAGTACAGGTGATTTGAGTTGTGAAACCTGTACCGTGACACAGGGTGGACTGATT
GGTTTAGTTGTGAGTAGTCTGTGCCCTATTATCTTGTCTATTCCTGTAAATGGTGGTCTAGCAGCCAGGTATGGATCAGC
ACTGTTACCAGATAAAGCAAACATCTTAACTTACTGGATCAGGATTTTTAAACCTGTCTTTAGAAAAATGTTATTTCCCA
TTTTACTTCACACTGCATTTGCAGCATACCTTGGATCTAGACAATATAAGCTACTCATAAAGGTTCTTCAGTTACCTGAA
CCTGACCTAAAA

ORF - retro_dord_656 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.24 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalNVLEYGSTYVGLNAAFCGLIANSLFRRVLNVTKAPVASGLPMAVIPFLTATVAYKGFVSLPLSTGDLSCE
NVLEYGSTYVGLNAAFCGLI.NSLFR..L.V.KAPVASGLP.AV.PFLTA.VAYKGFVSLPLSTGDLSCE
RetrocopyNVLEYGSTYVGLNAAFCGLIDNSLFRHALHVIKAPVASGLPIAVMPFLTANVAYKGFVSLPLSTGDLSCE
ParentalTCTVTRGGLIGLVVGSLYPIILAIPVNGGLAARYGSALLPDKANILTYWIRISKPVFRKMLFPILLQTTF
TCTVT.GGLIGLVV.SL.PIIL.IPVNGGLAARYGSALLPDKANILTYWIRI.KPVFRKMLFPILL.T.F
RetrocopyTCTVTQGGLIGLVVSSLCPIILSIPVNGGLAARYGSALLPDKANILTYWIRIFKPVFRKMLFPILLHTAF
ParentalAAYLGSRQYKLLIKALQLPEPDLK
AAYLGSRQYKLLIK.LQLPEPDLK
RetrocopyAAYLGSRQYKLLIKVLQLPEPDLK

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






RNA-Seq - click to see more details

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Dipodomys ordii was not studied using ChIP-Seq data.

EST - click to see more details

Dipodomys ordii was not studied using EST data.

TSS - click to see more details

Dipodomys ordii was not studied using FANTOM5 data.

Lab - click to see more details

retro_dord_656 was not experimentally validated.

Retrocopy orthology:
Dipodomys ordii 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 28 parental genes, and 80 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000087032 retrocopies
retro_amel_358, retro_amel_422,
Bos taurus ENSBTAG000000004512 retrocopies
retro_btau_1849, retro_btau_223,
Canis familiaris ENSCAFG000000309131 retrocopy
retro_cfam_725,
Callithrix jacchus ENSCJAG000000144661 retrocopy
retro_cjac_4040,
Dasypus novemcinctus ENSDNOG000000043917 retrocopies
retro_dnov_1741, retro_dnov_2634, retro_dnov_2676, retro_dnov_484, retro_dnov_549, retro_dnov_951, retro_dnov_984,
Dipodomys ordii ENSDORG00000006408 2 retrocopies
retro_dord_120, retro_dord_656 ,
Erinaceus europaeus ENSEEUG000000091053 retrocopies
retro_eeur_24, retro_eeur_340, retro_eeur_615,
Echinops telfairi ENSETEG000000071802 retrocopies
retro_etel_1693, retro_etel_667,
Felis catus ENSFCAG000000276063 retrocopies
retro_fcat_1015, retro_fcat_1320, retro_fcat_48,
Homo sapiens ENSG000001712022 retrocopies
retro_hsap_1510, retro_hsap_3306,
Gorilla gorilla ENSGGOG000000277422 retrocopies
retro_ggor_1157, retro_ggor_1308,
Macropus eugenii ENSMEUG000000116251 retrocopy
retro_meug_1914,
Microcebus murinus ENSMICG000000055103 retrocopies
retro_mmur_1382, retro_mmur_941, retro_mmur_956,
Myotis lucifugus ENSMLUG000000058963 retrocopies
retro_mluc_1150, retro_mluc_1290, retro_mluc_1951,
Macaca mulatta ENSMMUG000000165422 retrocopies
retro_mmul_2073, retro_mmul_2146,
Mustela putorius furoENSMPUG000000099682 retrocopies
retro_mputfur_1077, retro_mputfur_720,
Mus musculus ENSMUSG000000306153 retrocopies
retro_mmus_1431, retro_mmus_1531, retro_mmus_3555,
Nomascus leucogenys ENSNLEG000000164082 retrocopies
retro_nleu_1751, retro_nleu_2500,
Oryctolagus cuniculus ENSOCUG000000165341 retrocopy
retro_ocun_1120,
Otolemur garnettii ENSOGAG0000000540312 retrocopies
retro_ogar_1020, retro_ogar_2016, retro_ogar_2083, retro_ogar_2118, retro_ogar_2379, retro_ogar_26, retro_ogar_2825, retro_ogar_2883, retro_ogar_3054, retro_ogar_3385, retro_ogar_661, retro_ogar_787,
Pongo abelii ENSPPYG000000037392 retrocopies
retro_pabe_1258, retro_pabe_2726,
Pan troglodytes ENSPTRG000000041342 retrocopies
retro_ptro_1022, retro_ptro_2165,
Pteropus vampyrus ENSPVAG000000061972 retrocopies
retro_pvam_1411, retro_pvam_254,
Rattus norvegicus ENSRNOG000000227483 retrocopies
retro_rnor_1706, retro_rnor_2844, retro_rnor_918,
Ictidomys tridecemlineatus ENSSTOG000000161012 retrocopies
retro_itri_108, retro_itri_165,
Tupaia belangeri ENSTBEG000000091575 retrocopies
retro_tbel_3441, retro_tbel_3720, retro_tbel_3785, retro_tbel_4072, retro_tbel_4111,
Tarsius syrichta ENSTSYG000000090716 retrocopies
retro_tsyr_1371, retro_tsyr_1457, retro_tsyr_1934, retro_tsyr_580, retro_tsyr_735, retro_tsyr_974,
Tursiops truncatus ENSTTRG000000120082 retrocopies
retro_ttru_1091, retro_ttru_415,


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