RetrogeneDB ID:

retro_lafr_926

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_5:54831994..54832357(+)
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_926
CCCACAAAGAAGGGTGATAAGAAGAAGGTCCCTTCTGCTATCAATGAAGTGGTGACCAGATTGTACACCACCAACAGTAA
CAAGTCATCCATGTTGTGGCTTCAAGAAGCATGCCCCTTGAGCACTCAAGAAGCTCTGGAAATTTGCCATGAAGGAGATG
TGAACACCAGATGTGCTCACTGACATCAGGCTTAACAAAGTTGTCTTGGCCAAAGAAATAAGGAATGTCCCATACCATAT
CTGTGTACAGTTGTTCAGAAAATGTAATGAGGATGAAGATTCACCAAACAAGCTCTATACATTGATTACCTATGTACCTG
TCACCACTTTCAAAAACCTAAAGTAGTCAACGTGGGTGAAAAC

ORF - retro_lafr_926 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.22 %
Parental protein coverage: 98.4 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalPAKKGGEKKKGRSAINEVVTREYTINIHKR-IHGV-GFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNK
P.KKG..KKK..SAINEVVTR.YT.N..K..IH.V.GFKK.AP.ALK...KFAMKEM.TPDV..D.RLNK
RetrocopyPTKKG-DKKKVPSAINEVVTRLYTTNSNKS<IHVV<GFKKHAP*ALKKLWKFAMKEM*TPDVLTDIRLNK
ParentalAVWAKGIRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKNL-QTVNVDEN
.V.AK.IRNVPY.I.V.L.RK.NEDEDSPNKLYTL.TYVPVTTFKNL...VNV.EN
RetrocopyVVLAKEIRNVPYHICVQLFRKCNEDEDSPNKLYTLITYVPVTTFKNL<KVVNVGEN

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






Loxodonta africana was not studied using RNA-Seq expression data.
Loxodonta africana was not studied using ChIP-Seq data.
Loxodonta africana was not studied using EST data.
Loxodonta africana was not studied using FANTOM5 data.
retro_lafr_926 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
Ailuropoda melanoleuca ENSAMEG000000156472 retrocopies
Cavia porcellus ENSCPOG000000210315 retrocopies
Equus caballus ENSECAG0000002407913 retrocopies
Latimeria chalumnae ENSLACG000000136031 retrocopy
Loxodonta africana ENSLAFG00000027873 12 retrocopies
Macropus eugenii ENSMEUG000000009638 retrocopies
Myotis lucifugus ENSMLUG0000000250721 retrocopies
Monodelphis domestica ENSMODG000000017045 retrocopies
Mustela putorius furoENSMPUG000000121972 retrocopies
Otolemur garnettii ENSOGAG0000001449410 retrocopies
Ochotona princeps ENSOPRG0000000120434 retrocopies
Pongo abelii ENSPPYG000000258704 retrocopies
Pteropus vampyrus ENSPVAG0000001171617 retrocopies
Sarcophilus harrisii ENSSHAG000000117063 retrocopies
Sus scrofa ENSSSCG000000081704 retrocopies
Sus scrofa ENSSSCG000000251806 retrocopies
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,



Copyright © RetrogeneDB 2014-2017