RetrogeneDB ID:

retro_dord_429

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_17926:26208..26645(-)
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:ENSDORG00000009287
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_dord_429
GGCAGCTTTACCTGGGGCTCTGGGTGTTTTACTTGTAAAACAAGGATTATTTGACTCCAATGCATCCAGCAGTGAGCTGA
GCTGCCCCACACCAAGACCCCGGTGAAGAACTGCACTGAGCTCACTGATGCACACATCATACTGAGTGTGGTGCAAGCCA
CCCACTGGGCCCTGCTCTAGTCCACAAGAAGGGGCTAGGCTGACTCCCAGCTGGGAAAAGACTATAAACAAAGAAATAAT
TCAAGAAATTTCAGAAGAAACACAATAGGAGTAAGAATGCCAAAATCCTCAGTCTTTTGGAGGAGCAGTTCCAGTAAGCA
AGGCATTTGATCTGCATTGTATCAAGATCAGGCCAGTGTAGCTGAGCAGATGACTGTGTGCTAGAAGACAAAGAACTGGG
GTACTATTTGGGGAAGTTCAAGGCACGCAAAGGCAAA

ORF - retro_dord_429 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.38 %
Parental protein coverage: 67.28 %
Number of stop codons detected: 6
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDS-TPYRLWYESHYALPLGRKKGAKLTP
G.F.WGS.C.T.KTRII.........EL..TKT.VKNC..L.D..T.Y..W.............GA.LTP
RetrocopyGSFTWGSGCFTCKTRII*LQCIQQ*AELPHTKTPVKNCTELTDA>TSY*VWCKPPTGPCSSPQEGARLTP
ParentalEEEEILNK-KRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLR
..E...NK.K..KK.QKK...R.KNAKI.SLLEEQFQ....L.CI.SR.GQC..AD..VLE.KEL..YL.
RetrocopySWEKTINK>K*FKKFQKKHN-RSKNAKILSLLEEQFQ*ARHLICIVSRSGQCS*ADDCVLEDKELGYYLG
ParentalKIKARKGK
K.KARKGK
RetrocopyKFKARKGK

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_429 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 35 parental genes, and 220 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000156971 retrocopy
retro_acar_124,
Ailuropoda melanoleuca ENSAMEG000000141473 retrocopies
retro_amel_1883, retro_amel_373, retro_amel_972,
Bos taurus ENSBTAG000000152852 retrocopies
retro_btau_1388, retro_btau_1593,
Canis familiaris ENSCAFG000000047458 retrocopies
retro_cfam_1336, retro_cfam_1662, retro_cfam_1730, retro_cfam_2139, retro_cfam_2177, retro_cfam_261, retro_cfam_589, retro_cfam_791,
Choloepus hoffmanni ENSCHOG0000000878510 retrocopies
retro_chof_1197, retro_chof_1258, retro_chof_1466, retro_chof_1638, retro_chof_2066, retro_chof_2617, retro_chof_2633, retro_chof_274, retro_chof_331, retro_chof_951,
Callithrix jacchus ENSCJAG000000041975 retrocopies
retro_cjac_1068, retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Cavia porcellus ENSCPOG000000007233 retrocopies
retro_cpor_1099, retro_cpor_335, retro_cpor_621,
Dasypus novemcinctus ENSDNOG000000252363 retrocopies
retro_dnov_1717, retro_dnov_802, retro_dnov_908,
Dipodomys ordii ENSDORG00000009287 1 retrocopy
retro_dord_429 ,
Echinops telfairi ENSETEG0000000400213 retrocopies
retro_etel_1000, retro_etel_1063, retro_etel_1201, retro_etel_147, retro_etel_1495, retro_etel_1733, retro_etel_1864, retro_etel_1941, retro_etel_2050, retro_etel_2060, retro_etel_302, retro_etel_368, retro_etel_395,
Felis catus ENSFCAG000000229964 retrocopies
retro_fcat_1222, retro_fcat_200, retro_fcat_456, retro_fcat_962,
Homo sapiens ENSG000001429378 retrocopies
retro_hsap_1467, retro_hsap_1536, retro_hsap_1942, retro_hsap_2034, retro_hsap_2791, retro_hsap_3158, retro_hsap_3410, retro_hsap_635,
Gorilla gorilla ENSGGOG000000056455 retrocopies
retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Loxodonta africana ENSLAFG000000275963 retrocopies
retro_lafr_531, retro_lafr_647, retro_lafr_904,
Macropus eugenii ENSMEUG000000013881 retrocopy
retro_meug_119,
Microcebus murinus ENSMICG000000080244 retrocopies
retro_mmur_1180, retro_mmur_1434, retro_mmur_1501, retro_mmur_380,
Myotis lucifugus ENSMLUG0000000155930 retrocopies
retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta ENSMMUG000000152702 retrocopies
retro_mmul_275, retro_mmul_70,
Monodelphis domestica ENSMODG000000283891 retrocopy
retro_mdom_998,
Mustela putorius furoENSMPUG000000134856 retrocopies
retro_mputfur_334, retro_mputfur_337, retro_mputfur_493, retro_mputfur_780, retro_mputfur_908, retro_mputfur_986,
Mus musculus ENSMUSG0000004767533 retrocopies
retro_mmus_1003, retro_mmus_1067, retro_mmus_1184, retro_mmus_1694, retro_mmus_1755, retro_mmus_1796, retro_mmus_2001, retro_mmus_2002, retro_mmus_2003, retro_mmus_2031, retro_mmus_2132, retro_mmus_2173, retro_mmus_2264, retro_mmus_2732, retro_mmus_2772, retro_mmus_2847, retro_mmus_2861, retro_mmus_293, retro_mmus_2956, retro_mmus_2998, retro_mmus_3018, retro_mmus_3052, retro_mmus_3057, retro_mmus_3279, retro_mmus_3307, retro_mmus_3521, retro_mmus_364, retro_mmus_392, retro_mmus_548, retro_mmus_559, retro_mmus_596, retro_mmus_646, retro_mmus_876,
Nomascus leucogenys ENSNLEG000000141471 retrocopy
retro_nleu_34,
Oryctolagus cuniculus ENSOCUG000000124761 retrocopy
retro_ocun_168,
Otolemur garnettii ENSOGAG0000000692216 retrocopies
retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pongo abelii ENSPPYG000000014261 retrocopy
retro_pabe_147,
Pan troglodytes ENSPTRG000000006591 retrocopy
retro_ptro_30,
Pteropus vampyrus ENSPVAG0000000985910 retrocopies
retro_pvam_1285, retro_pvam_1315, retro_pvam_1345, retro_pvam_403, retro_pvam_419, retro_pvam_463, retro_pvam_514, retro_pvam_578, retro_pvam_685, retro_pvam_991,
Rattus norvegicus ENSRNOG000000187682 retrocopies
retro_rnor_222, retro_rnor_235,
Sorex araneus ENSSARG000000008991 retrocopy
retro_sara_462,
Sarcophilus harrisii ENSSHAG000000001115 retrocopies
retro_shar_408, retro_shar_472, retro_shar_480, retro_shar_636, retro_shar_667,
Sus scrofa ENSSSCG000000039304 retrocopies
retro_sscr_353, retro_sscr_550, retro_sscr_607, retro_sscr_919,
Ictidomys tridecemlineatus ENSSTOG000000063223 retrocopies
retro_itri_1337, retro_itri_1380, retro_itri_750,
Tupaia belangeri ENSTBEG0000000041820 retrocopies
retro_tbel_1066, retro_tbel_1537, retro_tbel_1538, retro_tbel_163, retro_tbel_1699, retro_tbel_2356, retro_tbel_244, retro_tbel_2580, retro_tbel_3058, retro_tbel_3230, retro_tbel_3478, retro_tbel_3905, retro_tbel_3950, retro_tbel_4241, retro_tbel_4250, retro_tbel_4530, retro_tbel_552, retro_tbel_803, retro_tbel_827, retro_tbel_934,
Tarsius syrichta ENSTSYG000000055255 retrocopies
retro_tsyr_1412, retro_tsyr_1507, retro_tsyr_2176, retro_tsyr_552, retro_tsyr_734,
Tursiops truncatus ENSTTRG000000033884 retrocopies
retro_ttru_1839, retro_ttru_282, retro_ttru_300, retro_ttru_344,


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