RetrogeneDB ID:

retro_lafr_987

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_57:13879719..13879976(+)
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:ENSLAFG00000006849
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_987
AAGGTCAGAATCATTGGTAAATATGGGACCTATTATGGTGCCTCTCTCAGGAAAATGGTGAAGAAAACTGAAATCGGCCA
GCAGGCCAAGAATGCTTGCTCCTTCTGTGACTAAATCAAAATGAAGAGACGACCTGTGGGGATCTGACAGTATAGTTCCT
GCTTGAAAACAGTAGCCGGTGGTGCCTGGTCCTACAGCACCACTTTGTAGTCACAGTAAAGTCTGGGATCAGAAGATGGA
GGTAATTGAAAGACCAG

ORF - retro_lafr_987 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.11 %
Parental protein coverage: 93.48 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKRRAVGIWHCGSCMKTVAGGAWTYNTT-S
KV.I.GKYGT.YGASLRKMVKK.EI.Q.AK..CSFC...KMKRR.VGI....SC.KTVAGGAW.Y.TT..
RetrocopyKVRIIGKYGTYYGASLRKMVKKTEIGQQAKNACSFCD*IKMKRRPVGI*QYSSCLKTVAGGAWSYSTT<F
ParentalAVTVKSAIRRLKELKDQ
.VTVKS.IRR...LKDQ
RetrocopyVVTVKSGIRRWR*LKDQ

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_987 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 10 parental genes, and 83 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000337724 retrocopies
Callithrix jacchus ENSCJAG000000124177 retrocopies
Equus caballus ENSECAG000000120466 retrocopies
Latimeria chalumnae ENSLACG000000115781 retrocopy
Loxodonta africana ENSLAFG00000006849 5 retrocopies
Macropus eugenii ENSMEUG0000000468023 retrocopies
Myotis lucifugus ENSMLUG000000007621 retrocopy
Otolemur garnettii ENSOGAG000000008173 retrocopies
Petromyzon marinus ENSPMAG000000000011 retrocopy
Pteropus vampyrus ENSPVAG0000000610212 retrocopies



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