RetrogeneDB ID:

retro_lafr_1171

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_8:44196106..44196405(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000030716
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSLAFG00000032173
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1171
TCTCTAGCGATCTCCAAGAATTTCCAGCACTTTTTGCAAGTACTGAACACTGACATCGATTGGTGGTGGAAAATAGCCTT
TGCCACCACTGCCATTAGGGTATGGGGTGAAGATATGCTCATGTGACATTGAGGAAAGCAGACATTGACTTCACCAAGAA
GATGGCAGAGATCACTGAGGATGTGGTGAAATGTGTGGTCACCATTATGCAGAATTCACACCAGTACAAGATTCTAGTCT
GGTTTTTGAACAGAGAGAAAGATGCAAACTATGGAAAATACAGTCAGGTTCTGGTCAAT

ORF - retro_lafr_1171 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.36 %
Parental protein coverage: 68.97 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIK-GVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
SL.I...FQH.L.VLNT.ID...KIAFA.TAI..G.G.RYAHV.LRKADID.TK...E.TED.V..V.TI
RetrocopySLAISKNFQHFLQVLNTDIDWWWKIAFATTAIR<GMG*RYAHVTLRKADIDFTKKMAEITEDVVKCVVTI
ParentalMQNPRQYKIPDWFLNRQKDVKDGKYSQVCID
MQN..QYKI..WFLNR.KD...GKYSQV...
RetrocopyMQNSHQYKILVWFLNREKDANYGKYSQVLVN

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_1171 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 36 parental genes, and 212 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000029181 retrocopy
retro_acar_206,
Ailuropoda melanoleuca ENSAMEG000000016232 retrocopies
retro_amel_1617, retro_amel_381,
Bos taurus ENSBTAG000000026482 retrocopies
retro_btau_1052, retro_btau_614,
Canis familiaris ENSCAFG000000009507 retrocopies
retro_cfam_1311, retro_cfam_1607, retro_cfam_2132, retro_cfam_414, retro_cfam_522, retro_cfam_789, retro_cfam_856,
Choloepus hoffmanni ENSCHOG000000037465 retrocopies
retro_chof_1248, retro_chof_1727, retro_chof_1768, retro_chof_1968, retro_chof_444,
Callithrix jacchus ENSCJAG000000103561 retrocopy
retro_cjac_3061,
Callithrix jacchus ENSCJAG000000216505 retrocopies
retro_cjac_22, retro_cjac_245, retro_cjac_2529, retro_cjac_2893, retro_cjac_2955,
Cavia porcellus ENSCPOG000000196754 retrocopies
retro_cpor_1044, retro_cpor_130, retro_cpor_860, retro_cpor_971,
Dasypus novemcinctus ENSDNOG0000001208413 retrocopies
retro_dnov_1295, retro_dnov_1398, retro_dnov_1448, retro_dnov_1675, retro_dnov_1770, retro_dnov_2008, retro_dnov_2115, retro_dnov_2223, retro_dnov_2288, retro_dnov_327, retro_dnov_363, retro_dnov_384, retro_dnov_399,
Dipodomys ordii ENSDORG000000138256 retrocopies
retro_dord_185, retro_dord_326, retro_dord_426, retro_dord_481, retro_dord_50, retro_dord_772,
Erinaceus europaeus ENSEEUG000000102978 retrocopies
retro_eeur_201, retro_eeur_261, retro_eeur_380, retro_eeur_460, retro_eeur_473, retro_eeur_498, retro_eeur_667, retro_eeur_689,
Felis catus ENSFCAG000000040137 retrocopies
retro_fcat_1058, retro_fcat_1536, retro_fcat_166, retro_fcat_222, retro_fcat_313, retro_fcat_327, retro_fcat_430,
Homo sapiens ENSG000002315002 retrocopies
retro_hsap_1806, retro_hsap_1974,
Gorilla gorilla ENSGGOG000000065715 retrocopies
retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana ENSLAFG00000032173 1 retrocopy
retro_lafr_1171 ,
Macropus eugenii ENSMEUG0000001677011 retrocopies
retro_meug_1296, retro_meug_1737, retro_meug_1807, retro_meug_1946, retro_meug_212, retro_meug_310, retro_meug_344, retro_meug_387, retro_meug_566, retro_meug_625, retro_meug_627,
Myotis lucifugus ENSMLUG000000073602 retrocopies
retro_mluc_181, retro_mluc_932,
Macaca mulatta ENSMMUG000000038671 retrocopy
retro_mmul_2198,
Monodelphis domestica ENSMODG000000142104 retrocopies
retro_mdom_1041, retro_mdom_1286, retro_mdom_1514, retro_mdom_642,
Mustela putorius furoENSMPUG000000023066 retrocopies
retro_mputfur_1110, retro_mputfur_1204, retro_mputfur_399, retro_mputfur_687, retro_mputfur_888, retro_mputfur_943,
Mus musculus ENSMUSG000000086682 retrocopies
retro_mmus_57, retro_mmus_66,
Nomascus leucogenys ENSNLEG0000000684010 retrocopies
retro_nleu_1074, retro_nleu_1161, retro_nleu_1176, retro_nleu_1466, retro_nleu_219, retro_nleu_2572, retro_nleu_2616, retro_nleu_525, retro_nleu_60, retro_nleu_737,
Oryctolagus cuniculus ENSOCUG000000105461 retrocopy
retro_ocun_31,
Otolemur garnettii ENSOGAG000000062257 retrocopies
retro_ogar_1498, retro_ogar_1832, retro_ogar_2372, retro_ogar_472, retro_ogar_608, retro_ogar_709, retro_ogar_905,
Procavia capensis ENSPCAG000000058542 retrocopies
retro_pcap_235, retro_pcap_319,
Pongo abelii ENSPPYG0000002595314 retrocopies
retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes ENSPTRG000000180391 retrocopy
retro_ptro_121,
Pteropus vampyrus ENSPVAG000000019026 retrocopies
retro_pvam_295, retro_pvam_556, retro_pvam_691, retro_pvam_708, retro_pvam_829, retro_pvam_875,
Rattus norvegicus ENSRNOG000000285054 retrocopies
retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii ENSSHAG000000068572 retrocopies
retro_shar_265, retro_shar_563,
Sarcophilus harrisii ENSSHAG000000086581 retrocopy
retro_shar_618,
Sus scrofa ENSSSCG000000015025 retrocopies
retro_sscr_112, retro_sscr_156, retro_sscr_157, retro_sscr_2, retro_sscr_831,
Ictidomys tridecemlineatus ENSSTOG0000000241713 retrocopies
retro_itri_1023, retro_itri_1049, retro_itri_1121, retro_itri_1316, retro_itri_1484, retro_itri_228, retro_itri_397, retro_itri_547, retro_itri_690, retro_itri_742, retro_itri_854, retro_itri_875, retro_itri_878,
Tupaia belangeri ENSTBEG0000001270840 retrocopies
retro_tbel_1070, retro_tbel_1739, retro_tbel_1745, retro_tbel_1806, retro_tbel_1818, retro_tbel_1827, retro_tbel_1855, retro_tbel_205, retro_tbel_2087, retro_tbel_211, retro_tbel_2299, retro_tbel_2309, retro_tbel_2312, retro_tbel_234, retro_tbel_2364, retro_tbel_2424, retro_tbel_2473, retro_tbel_250, retro_tbel_2682, retro_tbel_2768, retro_tbel_295, retro_tbel_3189, retro_tbel_3317, retro_tbel_3383, retro_tbel_3625, retro_tbel_363, retro_tbel_3686, retro_tbel_3731, retro_tbel_3870, retro_tbel_4100, retro_tbel_4215, retro_tbel_4365, retro_tbel_45, retro_tbel_4562, retro_tbel_4578, retro_tbel_462, retro_tbel_57, retro_tbel_578, retro_tbel_856, retro_tbel_941,
Tarsius syrichta ENSTSYG000000125088 retrocopies
retro_tsyr_1121, retro_tsyr_1307, retro_tsyr_1627, retro_tsyr_194, retro_tsyr_1949, retro_tsyr_2042, retro_tsyr_575, retro_tsyr_639,
Tursiops truncatus ENSTTRG000000043023 retrocopies
retro_ttru_1012, retro_ttru_1553, retro_ttru_837,


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