RetrogeneDB ID:

retro_lafr_685

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_3:96311193..96311739(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB1
Ensembl ID:ENSLAFG00000000269
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_685
GGCAAAGAAGCTCCTAAGAAGCCAAGAGGCAAAATGTGATCATATGCATTTTTTTTGTGCAAACTTGCGAGGAGGAGCAC
AAGAAGAAGCACCCAGATGCTTGTCAACTCAGAGTTTTCTAAGAAGTGCTCAGAGAACTAAAAGTCCATGTCTGCTAAAG
AGAAAAGGAAAGTTTTGAAGACATGGCAAAGGTGGACAAGGCCCATTACGTAAGAGAAATGAATGCCTATATCCCTCCTA
AAGTGGAAACAAAAAGAAATTCAAGGATCTCAATGCACCCAAGAGGATTCCTTTGGCCTTTTTCATGTTTTGTTCTGAGT
ATCACTCAAAAATCAAAGGCGAGCATTTAGGCCTATCCATTGGTGACATTGCAAAGAAACTTGGAGAGATGTGGAATAAT
ACTGCTGCCAGTGACAAGCAGTCTTACGAGAGGAAGGTCACTAAGGTGAAGGAGAAATATTAAAAGGATATTGCTGCATA
CCAGGGTAAAGAAAGCCTGATGCAGCCAAAAGGGGGGTGGTCAAGGCTGAAGAAAGCAAGAAAAAG

ORF - retro_lafr_685 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.66 %
Parental protein coverage: 85.12 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEK-GKF-EDMAKADKA
GK..PKKPRGKM.SYAFF................VN.SEFSKKCSE..K.MSAKEK.GKF.EDMAK.DKA
RetrocopyGKEAPKKPRGKM*SYAFFLCKLARRSTRRSTQMLVN-SEFSKKCSEN*KSMSAKEK>GKF>EDMAKVDKA
ParentalRYEREMKTYIPPKGETK-KKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAA
.Y.REM..YIPPK.ETK.KKFKD.NAPKR.P.AFF.FCSEY..KIKGEH.GLSIGD.AKKLGEMWNNTAA
RetrocopyHYVREMNAYIPPKVETK<KKFKDLNAPKRIPLAFFMFCSEYHSKIKGEHLGLSIGDIAKKLGEMWNNTAA
ParentalDDKQPYEKKAAKLKEKYEKDIAAYRAK-GKPDAAKKGVVKAEKSKKK
.DKQ.YE.K..K.KEKY.KDIAAY..K..KPDAAK.GVVKAE.SKKK
RetrocopySDKQSYERKVTKVKEKY*KDIAAYQGK<RKPDAAKRGVVKAEESKKK

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_685 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 27 parental genes, and 343 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000088807 retrocopies
Bos taurus ENSBTAG000000181032 retrocopies
Canis familiaris ENSCAFG0000000659713 retrocopies
Choloepus hoffmanni ENSCHOG0000000242316 retrocopies
Callithrix jacchus ENSCJAG0000002161511 retrocopies
Cavia porcellus ENSCPOG000000039851 retrocopy
Equus caballus ENSECAG000000084392 retrocopies
Echinops telfairi ENSETEG0000000404818 retrocopies
Felis catus ENSFCAG0000000020010 retrocopies
Gorilla gorilla ENSGGOG0000002676423 retrocopies
Loxodonta africana ENSLAFG00000000269 4 retrocopies
Loxodonta africana ENSLAFG000000104173 retrocopies
Loxodonta africana ENSLAFG000000258771 retrocopy
Macropus eugenii ENSMEUG000000013802 retrocopies
Microcebus murinus ENSMICG000000005731 retrocopy
Microcebus murinus ENSMICG000000071447 retrocopies
Macaca mulatta ENSMMUG000000233993 retrocopies
Monodelphis domestica ENSMODG0000000923814 retrocopies
Oryctolagus cuniculus ENSOCUG0000002133516 retrocopies
Otolemur garnettii ENSOGAG00000003205104 retrocopies
retro_ogar_1008, retro_ogar_1043, retro_ogar_106, retro_ogar_1133, retro_ogar_123, retro_ogar_1232, retro_ogar_1296, retro_ogar_1299, retro_ogar_1330, retro_ogar_1386, retro_ogar_1398, retro_ogar_1399, retro_ogar_1421, retro_ogar_1423, retro_ogar_1424, retro_ogar_1431, retro_ogar_1461, retro_ogar_1560, retro_ogar_1571, retro_ogar_1585, retro_ogar_1597, retro_ogar_1600, retro_ogar_1607, retro_ogar_1628, retro_ogar_163, retro_ogar_1664, retro_ogar_1698, retro_ogar_17, retro_ogar_172, retro_ogar_1738, retro_ogar_1758, retro_ogar_1781, retro_ogar_1843, retro_ogar_1844, retro_ogar_1861, retro_ogar_1867, retro_ogar_1878, retro_ogar_1894, retro_ogar_1896, retro_ogar_198, retro_ogar_1991, retro_ogar_2136, retro_ogar_2165, retro_ogar_219, retro_ogar_2282, retro_ogar_2318, retro_ogar_2319, retro_ogar_2352, retro_ogar_2385, retro_ogar_2403, retro_ogar_2429, retro_ogar_2436, retro_ogar_2458, retro_ogar_250, retro_ogar_2559, retro_ogar_2598, retro_ogar_2615, retro_ogar_2618, retro_ogar_2730, retro_ogar_2777, retro_ogar_2778, retro_ogar_2814, retro_ogar_2824, retro_ogar_2836, retro_ogar_284, retro_ogar_2845, retro_ogar_2891, retro_ogar_2894, retro_ogar_2906, retro_ogar_2961, retro_ogar_3008, retro_ogar_3018, retro_ogar_3028, retro_ogar_304, retro_ogar_311, retro_ogar_3136, retro_ogar_317, retro_ogar_320, retro_ogar_3208, retro_ogar_3230, retro_ogar_3325, retro_ogar_3330, retro_ogar_3355, retro_ogar_3374, retro_ogar_3500, retro_ogar_422, retro_ogar_435, retro_ogar_511, retro_ogar_542, retro_ogar_547, retro_ogar_634, retro_ogar_663, retro_ogar_698, retro_ogar_716, retro_ogar_772, retro_ogar_778, retro_ogar_8, retro_ogar_835, retro_ogar_890, retro_ogar_904, retro_ogar_912, retro_ogar_918, retro_ogar_92, retro_ogar_933,
Otolemur garnettii ENSOGAG000000321471 retrocopy
Ochotona princeps ENSOPRG000000035078 retrocopies
Pongo abelii ENSPPYG0000000554635 retrocopies
Rattus norvegicus ENSRNOG000000298131 retrocopy
Sorex araneus ENSSARG0000000447014 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000044319 retrocopies
Tarsius syrichta ENSTSYG000000063287 retrocopies



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