RetrogeneDB ID:

retro_lafr_245

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_10:39549470..39549815(-)
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:ENSLAFG00000027873
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_245
AAGAAGAAGGGCCATTCTGCTATCAAGGAGTGGTGACCAGAAAGTACACCATTAACATTTATAAGCGCACCCATGGAGTG
GGTTTAAAGAAGTGTGCCCCTTGGGCCCTCAAGGAGACCTGGAAATCTGCCACGAAGGAGATGAGAATGCCAGATGTGCC
CACCAACACCAAGCTCAACAAAGCTGTCTGGGCCAAAGGAATAAGGAATGTTCCATATCACATCCATGTATAGCGGTCCA
GAAAACAATGAGGATGAGGACTCATCAAACTAGCTCCATACACTGGTTACCTATGTACCCGTCACCACTTTCCAAAACCT
ACAGTCAGTCAGTGTGGATGAAAAT

ORF - retro_lafr_245 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.49 %
Parental protein coverage: 92.8 %
Number of stop codons detected: 2
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalKKKGRSAINE-VVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNKAVWAKGIR
KKKG.SAI.E.VVTR.YTINI.KR.HGVG.KK.AP.ALKE..K.A.KEM..PDV...T.LNKAVWAKGIR
RetrocopyKKKGHSAIKE<VVTRKYTINIYKRTHGVGLKKCAPWALKETWKSATKEMRMPDVPTNTKLNKAVWAKGIR
ParentalNVPYRIRVRLSRKR-NEDEDSPNKLYTLVTYVPVTTFKNLQTVNVDEN
NVPY.I.V..SRK.......S.N.L.TLVTYVPVTTF.NLQ.V.VDEN
RetrocopyNVPYHIHV*RSRKQ>EDEDSS-N*LHTLVTYVPVTTFQNLQSVSVDEN

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_245 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 18 parental genes, and 285 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000079141 retrocopy
retro_acar_168,
Ailuropoda melanoleuca ENSAMEG000000156472 retrocopies
retro_amel_12, retro_amel_222,
Cavia porcellus ENSCPOG000000210315 retrocopies
retro_cpor_1184, retro_cpor_170, retro_cpor_190, retro_cpor_341, retro_cpor_366,
Equus caballus ENSECAG0000002407913 retrocopies
retro_ecab_1034, retro_ecab_1102, retro_ecab_163, retro_ecab_206, retro_ecab_259, retro_ecab_332, retro_ecab_397, retro_ecab_414, retro_ecab_448, retro_ecab_451, retro_ecab_499, retro_ecab_812, retro_ecab_972,
Latimeria chalumnae ENSLACG000000136031 retrocopy
retro_lcha_94,
Loxodonta africana ENSLAFG00000027873 12 retrocopies
retro_lafr_118, retro_lafr_187, retro_lafr_20, retro_lafr_245 , retro_lafr_307, retro_lafr_56, retro_lafr_663, retro_lafr_703, retro_lafr_710, retro_lafr_778, retro_lafr_885, retro_lafr_926,
Macropus eugenii ENSMEUG000000009638 retrocopies
retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Myotis lucifugus ENSMLUG0000000250721 retrocopies
retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Monodelphis domestica ENSMODG000000017045 retrocopies
retro_mdom_1052, retro_mdom_1464, retro_mdom_1674, retro_mdom_1720, retro_mdom_1818,
Mustela putorius furoENSMPUG000000121972 retrocopies
retro_mputfur_50, retro_mputfur_71,
Otolemur garnettii ENSOGAG0000001449410 retrocopies
retro_ogar_103, retro_ogar_143, retro_ogar_150, retro_ogar_178, retro_ogar_181, retro_ogar_186, retro_ogar_262, retro_ogar_271, retro_ogar_29, retro_ogar_3,
Ochotona princeps ENSOPRG0000000120434 retrocopies
retro_opri_1032, retro_opri_1059, retro_opri_1081, retro_opri_1108, retro_opri_1117, retro_opri_113, retro_opri_1176, retro_opri_1177, retro_opri_132, retro_opri_152, retro_opri_179, retro_opri_213, retro_opri_236, retro_opri_259, retro_opri_346, retro_opri_411, retro_opri_435, retro_opri_531, retro_opri_561, retro_opri_572, retro_opri_58, retro_opri_588, retro_opri_602, retro_opri_677, retro_opri_710, retro_opri_744, retro_opri_796, retro_opri_803, retro_opri_804, retro_opri_811, retro_opri_819, retro_opri_909, retro_opri_915, retro_opri_93,
Pongo abelii ENSPPYG000000258704 retrocopies
retro_pabe_106, retro_pabe_1635, retro_pabe_168, retro_pabe_895,
Pteropus vampyrus ENSPVAG0000001171617 retrocopies
retro_pvam_1131, retro_pvam_1265, retro_pvam_1359, retro_pvam_197, retro_pvam_349, retro_pvam_410, retro_pvam_441, retro_pvam_469, retro_pvam_484, retro_pvam_501, retro_pvam_565, retro_pvam_606, retro_pvam_631, retro_pvam_65, retro_pvam_815, retro_pvam_861, retro_pvam_864,
Sarcophilus harrisii ENSSHAG000000117063 retrocopies
retro_shar_190, retro_shar_285, retro_shar_721,
Sus scrofa ENSSSCG000000081704 retrocopies
retro_sscr_1072, retro_sscr_1073, retro_sscr_128, retro_sscr_263,
Sus scrofa ENSSSCG000000251806 retrocopies
retro_sscr_20, retro_sscr_34, retro_sscr_469, retro_sscr_501, retro_sscr_713, retro_sscr_81,
Tupaia belangeri ENSTBEG00000016254137 retrocopies
retro_tbel_1092, retro_tbel_1129, retro_tbel_115, retro_tbel_1176, retro_tbel_1195, retro_tbel_1226, retro_tbel_1239, retro_tbel_1249, retro_tbel_1254, retro_tbel_1258, retro_tbel_1266, retro_tbel_131, retro_tbel_1310, retro_tbel_1334, retro_tbel_1356, retro_tbel_1368, retro_tbel_1369, retro_tbel_1381, retro_tbel_1402, retro_tbel_1414, retro_tbel_1423, retro_tbel_1437, retro_tbel_1454, retro_tbel_1574, retro_tbel_1593, retro_tbel_1597, retro_tbel_1605, retro_tbel_1611, retro_tbel_1612, retro_tbel_1632, retro_tbel_1768, retro_tbel_1797, retro_tbel_1802, retro_tbel_184, retro_tbel_189, retro_tbel_1890, retro_tbel_1897, retro_tbel_1915, retro_tbel_2024, retro_tbel_2027, retro_tbel_2050, retro_tbel_2069, retro_tbel_2093, retro_tbel_2140, retro_tbel_2159, retro_tbel_2233, retro_tbel_2341, retro_tbel_2359, retro_tbel_2382, retro_tbel_246, retro_tbel_2520, retro_tbel_2531, retro_tbel_2581, retro_tbel_2582, retro_tbel_2614, retro_tbel_2625, retro_tbel_2668, retro_tbel_2692, retro_tbel_2709, retro_tbel_2741, retro_tbel_2789, retro_tbel_2825, retro_tbel_2847, retro_tbel_2930, retro_tbel_2951, retro_tbel_3015, retro_tbel_3028, retro_tbel_3035, retro_tbel_3061, retro_tbel_3077, retro_tbel_3154, retro_tbel_3174, retro_tbel_3222, retro_tbel_3274, retro_tbel_3282, retro_tbel_3292, retro_tbel_3346, retro_tbel_3365, retro_tbel_337, retro_tbel_3378, retro_tbel_3425, retro_tbel_3442, retro_tbel_3484, retro_tbel_3500, retro_tbel_3519, retro_tbel_3578, retro_tbel_3580, retro_tbel_3618, retro_tbel_3637, retro_tbel_3710, retro_tbel_3722, retro_tbel_3745, retro_tbel_3775, retro_tbel_3780, retro_tbel_3794, retro_tbel_3801, retro_tbel_381, retro_tbel_3812, retro_tbel_3846, retro_tbel_3869, retro_tbel_3873, retro_tbel_398, retro_tbel_3982, retro_tbel_3996, retro_tbel_4033, retro_tbel_4069, retro_tbel_4158, retro_tbel_4161, retro_tbel_4174, retro_tbel_4235, retro_tbel_4247, retro_tbel_4286, retro_tbel_4297, retro_tbel_4363, retro_tbel_4374, retro_tbel_461, retro_tbel_4612, retro_tbel_4646, retro_tbel_466, retro_tbel_488, retro_tbel_503, retro_tbel_510, retro_tbel_577, retro_tbel_599, retro_tbel_626, retro_tbel_696, retro_tbel_718, retro_tbel_741, retro_tbel_744, retro_tbel_780, retro_tbel_788, retro_tbel_872, retro_tbel_886, retro_tbel_891, retro_tbel_908, retro_tbel_914, retro_tbel_942,


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