RetrogeneDB ID:

retro_dord_314

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_11262:20976..21525(+)
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:ENSDORG00000002250
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_dord_314
AGATCACTAGTTATGAGGACTCAATGAATCAAAATCCCATCTGATGATGTCAAGTGCTGGATGTTTAAAGTGAGCCTTCC
TGATCTGCAGAAAGATGAAGTTGCATGTAGAAAACTCAAGCTAATTACTGAGGTTGTTCAGGGCAAGAAGTGCCTGACCA
ACTTCTATGACATAGATCTCACCTGAGGTACAGTGTGCTCCATGGTCAAAAAGTGGCAGGCCATGATTGAAGCTCATGTT
GATGCCAGACTGCAGGTGGTTATTTGCTTCCTTTGTTTGGTGTTGGTTTCACTAAAAGATTCAACAATCAGATACCCAAG
ACCCTCTTGTGCTCAGCAACAACAGGCCTGCCAAACCTGGAAGAAAATCATAGAAATCATGATAGGAGAAGCACAGACAA
ATGACTTGAAAGAAGTACTTCATAATTTGATTCCAGACAGCATTGGGAAAGTCATAGAAAAGGATTGTCAGTCTACTCAT
TATGTCTTCCTTAGAAAAGTAGTACTGCTGAAGAAGCTCGAATTTGAATTGGGAGAACTCACAGAACTC

ORF - retro_dord_314 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.43 %
Parental protein coverage: 70.72 %
Number of stop codons detected: 2
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVK
..LV.RTQ..KI.SD..K...F.VSL.DLQ.DEVA.RK.KLITE.VQGK.CLTNF...DLT....CSMVK
RetrocopyRSLVMRTQ*IKIPSDDVKCWMFKVSLPDLQKDEVACRKLKLITEVVQGKKCLTNFYDIDLT*GTVCSMVK
ParentalKWQTMIEAHVDVK-TTDGYLLRLFCVGFTKKRNNQIRKT-SYAQHQQVRQIRKKMMEIMTREVQTNDLKE
KWQ.MIEAHVD...T..GYLL.LF.VGFTK..NNQI.KT.S.AQ.QQ..Q..KK..EIM..E.QTNDLKE
RetrocopyKWQAMIEAHVDAR<TAGGYLLPLFGVGFTKRFNNQIPKT>SCAQQQQACQTWKKIIEIMIGEAQTNDLKE
ParentalVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMEL
V...LIPDSIGK.IEK.CQS....H.VF.RKV..LKK..FELG.L.EL
RetrocopyVLHNLIPDSIGKVIEKDCQS---THYVFLRKVVLLKKLEFELGELTEL

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_314 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 21 parental genes, and 187 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000099083 retrocopies
retro_btau_1284, retro_btau_1733, retro_btau_233,
Canis familiaris ENSCAFG000000079907 retrocopies
retro_cfam_103, retro_cfam_146, retro_cfam_169, retro_cfam_170, retro_cfam_179, retro_cfam_222, retro_cfam_77,
Callithrix jacchus ENSCJAG000000022687 retrocopies
retro_cjac_2, retro_cjac_21, retro_cjac_249, retro_cjac_312, retro_cjac_337, retro_cjac_368, retro_cjac_78,
Cavia porcellus ENSCPOG000000155699 retrocopies
retro_cpor_1154, retro_cpor_1229, retro_cpor_210, retro_cpor_383, retro_cpor_460, retro_cpor_555, retro_cpor_609, retro_cpor_646, retro_cpor_789,
Dipodomys ordii ENSDORG00000002250 10 retrocopies
retro_dord_142, retro_dord_168, retro_dord_193, retro_dord_209, retro_dord_229, retro_dord_314 , retro_dord_380, retro_dord_752, retro_dord_757, retro_dord_95,
Equus caballus ENSECAG000000095736 retrocopies
retro_ecab_168, retro_ecab_222, retro_ecab_256, retro_ecab_597, retro_ecab_626, retro_ecab_885,
Erinaceus europaeus ENSEEUG000000049944 retrocopies
retro_eeur_297, retro_eeur_510, retro_eeur_517, retro_eeur_66,
Felis catus ENSFCAG000000312885 retrocopies
retro_fcat_1110, retro_fcat_134, retro_fcat_1878, retro_fcat_780, retro_fcat_858,
Gorilla gorilla ENSGGOG000000031822 retrocopies
retro_ggor_70, retro_ggor_97,
Loxodonta africana ENSLAFG000000176603 retrocopies
retro_lafr_10, retro_lafr_38, retro_lafr_385,
Myotis lucifugus ENSMLUG000000147888 retrocopies
retro_mluc_1197, retro_mluc_1397, retro_mluc_1568, retro_mluc_1846, retro_mluc_2130, retro_mluc_2158, retro_mluc_2388, retro_mluc_862,
Macaca mulatta ENSMMUG000000218211 retrocopy
retro_mmul_2297,
Monodelphis domestica ENSMODG000000009696 retrocopies
retro_mdom_1040, retro_mdom_1229, retro_mdom_1396, retro_mdom_1480, retro_mdom_627, retro_mdom_694,
Mustela putorius furoENSMPUG000000071398 retrocopies
retro_mputfur_1293, retro_mputfur_1363, retro_mputfur_278, retro_mputfur_316, retro_mputfur_504, retro_mputfur_695, retro_mputfur_764, retro_mputfur_847,
Mus musculus ENSMUSG000000280812 retrocopies
retro_mmus_218, retro_mmus_254,
Oryctolagus cuniculus ENSOCUG000000070111 retrocopy
retro_ocun_257,
Rattus norvegicus ENSRNOG000000118931 retrocopy
retro_rnor_198,
Sarcophilus harrisii ENSSHAG000000150882 retrocopies
retro_shar_777, retro_shar_95,
Sus scrofa ENSSSCG000000090193 retrocopies
retro_sscr_27, retro_sscr_749, retro_sscr_762,
Ictidomys tridecemlineatus ENSSTOG000000242031 retrocopy
retro_itri_58,
Tupaia belangeri ENSTBEG0000000296398 retrocopies
retro_tbel_1005, retro_tbel_11, retro_tbel_1119, retro_tbel_116, retro_tbel_1232, retro_tbel_1318, retro_tbel_133, retro_tbel_137, retro_tbel_1375, retro_tbel_1378, retro_tbel_1383, retro_tbel_1417, retro_tbel_1421, retro_tbel_1509, retro_tbel_1686, retro_tbel_1698, retro_tbel_172, retro_tbel_1720, retro_tbel_1721, retro_tbel_1744, retro_tbel_1814, retro_tbel_1829, retro_tbel_1856, retro_tbel_1896, retro_tbel_1948, retro_tbel_1960, retro_tbel_1999, retro_tbel_206, retro_tbel_2200, retro_tbel_2306, retro_tbel_2463, retro_tbel_2483, retro_tbel_2510, retro_tbel_2626, retro_tbel_2654, retro_tbel_2657, retro_tbel_2745, retro_tbel_2759, retro_tbel_2760, retro_tbel_2764, retro_tbel_281, retro_tbel_2857, retro_tbel_2957, retro_tbel_2959, retro_tbel_3114, retro_tbel_317, retro_tbel_3212, retro_tbel_3255, retro_tbel_3259, retro_tbel_3299, retro_tbel_336, retro_tbel_3372, retro_tbel_3416, retro_tbel_3471, retro_tbel_3486, retro_tbel_3513, retro_tbel_3558, retro_tbel_3613, retro_tbel_3631, retro_tbel_3655, retro_tbel_3705, retro_tbel_373, retro_tbel_375, retro_tbel_3755, retro_tbel_3786, retro_tbel_3815, retro_tbel_3823, retro_tbel_3832, retro_tbel_386, retro_tbel_3882, retro_tbel_39, retro_tbel_3947, retro_tbel_3966, retro_tbel_399, retro_tbel_4116, retro_tbel_4144, retro_tbel_4147, retro_tbel_4211, retro_tbel_4220, retro_tbel_423, retro_tbel_4294, retro_tbel_4304, retro_tbel_4347, retro_tbel_438, retro_tbel_4428, retro_tbel_445, retro_tbel_4579, retro_tbel_598, retro_tbel_619, retro_tbel_623, retro_tbel_671, retro_tbel_859, retro_tbel_90, retro_tbel_912, retro_tbel_92, retro_tbel_928, retro_tbel_956, retro_tbel_973,


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