RetrogeneDB ID:

retro_lafr_908

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_48:14178891..14179353(-)
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:ENSLAFG00000013387
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_908
ATGGCACCAAAAGTGAAGAAGGAAGCCCCTGCTCCTCCCAGAACTGAACCAAAGCAAAGGCTTTGAAGGCCAAGAGGGCA
GTGCTGAATGGCATTCACAGCCACACACACAAAAATATCCGCATGTCACCTGTCTTCCAGTGGCCCAAGACACCGCAGCT
CTGAAGGCAGCCCAAATATTCTCGAAGAGAGCCCCCAGGAGAAATAAGCTTGACCACTATGCCATCATCAAGTTTCTCCG
ACTGTTGACTCGGCCATGAAGAAGATCGAAGATAACAACACACTTGTGTTTGTTGTGGATGTCAACGCCAACAAACACCA
GATGGAACAGGCTGTGAAGAAGCTCTATGGCATGGATGTGGCCAAGGTCAACACCCTAATCAGGCCTGATGGAGAGAAGG
TATAGGTTTGACTGGCTCCTGGTGGTGATGCTTTGAATATTGCCAACAAAATTTGGATCATC

ORF - retro_lafr_908 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.84 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAPKAKKEAPAPPKTE-AKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPR-KSAPRR
MAPK.KKEAPAPP.TE..KAKALKAK.AVL.G.HSH..K.IR.SP.F..PKT..L.RQPKY.R.K.APRR
RetrocopyMAPKVKKEAPAPPRTE<TKAKALKAKRAVLNGIHSHTHKNIRMSPVFQWPKTPQL*RQPKYSR<KRAPRR
ParentalNKLDHYAIIKF-PLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAY
NKLDHYAIIKF...T..SAMKKIEDNNTLVF.VDV.ANKHQ..QAVKKLY..DVAKVNTLIRPDGEK...
RetrocopyNKLDHYAIIKF<SPTVDSAMKKIEDNNTLVFVVDVNANKHQMEQAVKKLYGMDVAKVNTLIRPDGEK-V*
ParentalVRLAPDYDALDVANKIGII
V.LAP..DAL..ANKI.II
RetrocopyV*LAPGGDALNIANKIWII

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_908 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 26 parental genes, and 564 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000053112 retrocopies
Ailuropoda melanoleuca ENSAMEG0000000468431 retrocopies
Bos taurus ENSBTAG000000463946 retrocopies
Callithrix jacchus ENSCJAG000000131267 retrocopies
Cavia porcellus ENSCPOG000000014526 retrocopies
Dasypus novemcinctus ENSDNOG0000001948765 retrocopies
Dipodomys ordii ENSDORG0000000097410 retrocopies
Equus caballus ENSECAG000000089281 retrocopy
Felis catus ENSFCAG0000000402135 retrocopies
Homo sapiens ENSG0000019824257 retrocopies
Gorilla gorilla ENSGGOG0000001673626 retrocopies
Loxodonta africana ENSLAFG00000013387 16 retrocopies
Myotis lucifugus ENSMLUG000000124484 retrocopies
Monodelphis domestica ENSMODG000000192973 retrocopies
Mustela putorius furoENSMPUG0000001417912 retrocopies
Mus musculus ENSMUSG000000585468 retrocopies
Nomascus leucogenys ENSNLEG0000000287260 retrocopies
Ochotona princeps ENSOPRG0000001262049 retrocopies
Procavia capensis ENSPCAG0000001700230 retrocopies
Pongo abelii ENSPPYG0000000810849 retrocopies
Pteropus vampyrus ENSPVAG0000000292232 retrocopies
Rattus norvegicus ENSRNOG000000233446 retrocopies
Sarcophilus harrisii ENSSHAG0000001454913 retrocopies
Sus scrofa ENSSSCG000000177689 retrocopies
Sus scrofa ENSSSCG000000298024 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000001132823 retrocopies



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