RetrogeneDB ID:

retro_lafr_185

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_1:49585200..49585618(+)
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:ENSLAFG00000023133
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_185
GAGATTCAGCCCTCAGGTACAATAGAAAATGTAAAAGCCAAGATCCAGGCTAAGGGAAGAATCCCTCCTATCAGCACAGA
CTGATCTTTCCTGGCAGATAACTGGAAGATGGACATAATTTGTCCAACTACAACATTCAAAAGGAGTTCACTCTTCATCT
TGTGTTGAGACTTTGTGGTGATGCTAAGAAAAAGAAGTAGTTTTACATTACTCCCAAGAAGAATGAGCATAAGAGAAAGA
AGGTTAAGCTGGCTGTCCTAAAATACTATAGGGTAGATAAGAATGGCAAAATTAGTTGCCTTCATTGCTAGTGCCTTTCA
GACGAATGTGGTACTGGAGTTTTGATGGCCAATCATGTTGGCAGACATTACTGTGGCAAGTGTTGTCTGACTATTGCTTC
GGCAAACCAGAAGACAAG

ORF - retro_lafr_185 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.92 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalQVEPSDTIENVKAKIQDKEGKRWIPPD-QQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGAKKRK
...PS.TIENVKAKIQ....K..IPP..Q.RLIF.G..LEDG..LS.YNIQKE.TLHLVLRL.G.AKK.K
RetrocopyEIQPSGTIENVKAKIQ---AKGRIPPI<QHRLIFPGR*LEDGHNLSNYNIQKEFTLHLVLRLCGDAKK-K
ParentalKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMASHFDRHYCGKCCLT-YCF
K..Y.TPKKN.HKRKKVKLAVLKYY.VD.NGKIS.L...C.SDECG.GV.MA.H..RHYCGKCCLT.YCF
RetrocopyK*FYITPKKNEHKRKKVKLAVLKYYRVDKNGKISCLHC*CLSDECGTGVLMANHVGRHYCGKCCLT<YCF
ParentalNKPEDK
.KPEDK
RetrocopyGKPEDK

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






RNA-Seq - click to see more details

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Loxodonta africana was not studied using ChIP-Seq data.

EST - click to see more details

Loxodonta africana was not studied using EST data.

TSS - click to see more details

Loxodonta africana was not studied using FANTOM5 data.

Lab - click to see more details

retro_lafr_185 was not experimentally validated.

Retrocopy orthology:
Loxodonta africana 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 29 parental genes, and 187 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000040175 retrocopies
retro_amel_1565, retro_amel_175, retro_amel_598, retro_amel_661, retro_amel_844,
Bos taurus ENSBTAG000000154736 retrocopies
retro_btau_1115, retro_btau_1213, retro_btau_1631, retro_btau_395, retro_btau_440, retro_btau_664,
Canis familiaris ENSCAFG000000234713 retrocopies
retro_cfam_1048, retro_cfam_640, retro_cfam_81,
Callithrix jacchus ENSCJAG000000100525 retrocopies
retro_cjac_200, retro_cjac_229, retro_cjac_344, retro_cjac_74, retro_cjac_88,
Cavia porcellus ENSCPOG000000058197 retrocopies
retro_cpor_1040, retro_cpor_1433, retro_cpor_406, retro_cpor_409, retro_cpor_502, retro_cpor_591, retro_cpor_990,
Dasypus novemcinctus ENSDNOG0000000481312 retrocopies
retro_dnov_131, retro_dnov_1340, retro_dnov_1432, retro_dnov_1558, retro_dnov_1664, retro_dnov_2022, retro_dnov_2183, retro_dnov_2576, retro_dnov_2635, retro_dnov_491, retro_dnov_538, retro_dnov_771,
Equus caballus ENSECAG000000187733 retrocopies
retro_ecab_341, retro_ecab_748, retro_ecab_776,
Erinaceus europaeus ENSEEUG000000023299 retrocopies
retro_eeur_127, retro_eeur_143, retro_eeur_193, retro_eeur_283, retro_eeur_289, retro_eeur_308, retro_eeur_58, retro_eeur_629, retro_eeur_72,
Felis catus ENSFCAG000000239391 retrocopy
retro_fcat_1542,
Homo sapiens ENSG0000014394710 retrocopies
retro_hsap_1694, retro_hsap_1715, retro_hsap_2217, retro_hsap_2416, retro_hsap_276, retro_hsap_3344, retro_hsap_3508, retro_hsap_4272, retro_hsap_4649, retro_hsap_4650,
Gorilla gorilla ENSGGOG000000076789 retrocopies
retro_ggor_1290, retro_ggor_1291, retro_ggor_1502, retro_ggor_1749, retro_ggor_179, retro_ggor_203, retro_ggor_2373, retro_ggor_2858, retro_ggor_2885,
Loxodonta africana ENSLAFG00000023133 2 retrocopies
retro_lafr_1122, retro_lafr_185 ,
Macropus eugenii ENSMEUG0000000891713 retrocopies
retro_meug_107, retro_meug_1184, retro_meug_1460, retro_meug_1514, retro_meug_1544, retro_meug_1657, retro_meug_183, retro_meug_1866, retro_meug_209, retro_meug_521, retro_meug_594, retro_meug_937, retro_meug_94,
Myotis lucifugus ENSMLUG0000001706410 retrocopies
retro_mluc_1201, retro_mluc_1255, retro_mluc_1298, retro_mluc_1646, retro_mluc_1730, retro_mluc_1865, retro_mluc_1867, retro_mluc_2264, retro_mluc_37, retro_mluc_380,
Myotis lucifugus ENSMLUG000000294491 retrocopy
retro_mluc_1585,
Macaca mulatta ENSMMUG000000155638 retrocopies
retro_mmul_1198, retro_mmul_193, retro_mmul_2189, retro_mmul_222, retro_mmul_2470, retro_mmul_282, retro_mmul_606, retro_mmul_73,
Monodelphis domestica ENSMODG000000018193 retrocopies
retro_mdom_1367, retro_mdom_1751, retro_mdom_205,
Mustela putorius furoENSMPUG000000104686 retrocopies
retro_mputfur_1512, retro_mputfur_242, retro_mputfur_319, retro_mputfur_332, retro_mputfur_499, retro_mputfur_777,
Mus musculus ENSMUSG0000002046019 retrocopies
retro_mmus_1074, retro_mmus_1268, retro_mmus_1440, retro_mmus_1441, retro_mmus_1815, retro_mmus_1917, retro_mmus_2043, retro_mmus_2092, retro_mmus_2098, retro_mmus_2449, retro_mmus_2514, retro_mmus_2785, retro_mmus_2801, retro_mmus_2931, retro_mmus_306, retro_mmus_318, retro_mmus_3234, retro_mmus_3292, retro_mmus_3391,
Oryctolagus cuniculus ENSOCUG0000000361310 retrocopies
retro_ocun_1087, retro_ocun_1163, retro_ocun_1209, retro_ocun_1259, retro_ocun_1268, retro_ocun_1339, retro_ocun_164, retro_ocun_288, retro_ocun_381, retro_ocun_851,
Ochotona princeps ENSOPRG0000001046913 retrocopies
retro_opri_1056, retro_opri_1120, retro_opri_162, retro_opri_177, retro_opri_191, retro_opri_331, retro_opri_472, retro_opri_490, retro_opri_582, retro_opri_71, retro_opri_717, retro_opri_801, retro_opri_871,
Pongo abelii ENSPPYG000000258711 retrocopy
retro_pabe_117,
Pan troglodytes ENSPTRG000000119281 retrocopy
retro_ptro_32,
Pteropus vampyrus ENSPVAG000000164713 retrocopies
retro_pvam_1052, retro_pvam_676, retro_pvam_952,
Rattus norvegicus ENSRNOG000000044262 retrocopies
retro_rnor_117, retro_rnor_161,
Sus scrofa ENSSSCG000000223571 retrocopy
retro_sscr_145,
Ictidomys tridecemlineatus ENSSTOG000000095665 retrocopies
retro_itri_1583, retro_itri_1765, retro_itri_26, retro_itri_635, retro_itri_962,
Tarsius syrichta ENSTSYG0000000084514 retrocopies
retro_tsyr_107, retro_tsyr_122, retro_tsyr_1379, retro_tsyr_1493, retro_tsyr_1520, retro_tsyr_1877, retro_tsyr_1890, retro_tsyr_1892, retro_tsyr_1950, retro_tsyr_2121, retro_tsyr_339, retro_tsyr_767, retro_tsyr_855, retro_tsyr_879,
Tursiops truncatus ENSTTRG000000139475 retrocopies
retro_ttru_1199, retro_ttru_1279, retro_ttru_533, retro_ttru_705, retro_ttru_838,


Copyright © RetrogeneDB 2014-2017