RetrogeneDB ID:

retro_lafr_1215

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_9:35390574..35390885(+)
Located in intron of:ENSLAFG00000021369
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SKA2
Ensembl ID:ENSLAFG00000003405
Aliases:None
Description:spindle and kinetochore associated complex subunit 2 [Source:HGNC Symbol;Acc:28006]


Retrocopy-Parental alignment summary:






>retro_lafr_1215
GCTGATTCTGATTTGGATTGTATTCTGTACAAGCTGGAATATGAAACCAGAACAATTATCCTGATGCTGCTGGTGTGAAA
AATCCTGTTACACTCTTAAAGGAATTGTCAGCAGTAAAGTCTCAATATCAGACTTTGCATACATGGTTTAAACCAACTGC
TTTTGAACAGAAAGAGACAAAGGGCTACATTTGTGTTACTTTGAACAAGACTATGACCATGATACAAGAACTACAAAAGC
TAACAGACCTGGAGCTGTCACCACTGACTGAAGAAAACTGCAGAAAAGCAATTAAAGTCTTAATGCCAGAC

ORF - retro_lafr_1215 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.83 %
Parental protein coverage: 97.25 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalADSDLDCILYRLEYEIK-NNHPDSAGAKNPVTLLKELSAIKSRYQTLHTRFKPIAVEQKKTKDHICVTLN
ADSDLDCILY.LEYE...NN.PD.AG.KNPVTLLKELSA.KS.YQTLHT.FKP.A.EQK.TK..ICVTLN
RetrocopyADSDLDCILYKLEYETR<NNYPDAAGVKNPVTLLKELSAVKSQYQTLHTWFKPTAFEQKETKGYICVTLN
ParentalKTMTMIQELRKLIELELLPLTEEEETAEKQLKAHMPD
KTMTMIQEL.KL..LEL.PLT..EE...K..K..MPD
RetrocopyKTMTMIQELQKLTDLELSPLT--EENCRKAIKVLMPD

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_1215 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 32 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000216802 retrocopies
Canis familiaris ENSCAFG000000292331 retrocopy
Cavia porcellus ENSCPOG000000060511 retrocopy
Dipodomys ordii ENSDORG000000107682 retrocopies
Equus caballus ENSECAG000000150071 retrocopy
Felis catus ENSFCAG000000228021 retrocopy
Homo sapiens ENSG000001826281 retrocopy
Loxodonta africana ENSLAFG00000003405 1 retrocopy
retro_lafr_1215 ,
Myotis lucifugus ENSMLUG000000109421 retrocopy
Monodelphis domestica ENSMODG000000146191 retrocopy
Mustela putorius furoENSMPUG000000152411 retrocopy
Mus musculus ENSMUSG000000204922 retrocopies
Otolemur garnettii ENSOGAG000000260724 retrocopies
Rattus norvegicus ENSRNOG000000259813 retrocopies
Sorex araneus ENSSARG000000111282 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000241694 retrocopies
Tarsius syrichta ENSTSYG000000061583 retrocopies
Tursiops truncatus ENSTTRG000000171961 retrocopy



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