RetrogeneDB ID:

retro_lafr_763

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_36:4336590..4337057(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ARPC3
Ensembl ID:ENSLAFG00000006166
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_763
CTGCCTATCAAAGGACTTATCAAAGGACGCACCCCTTGAGAGACAAAAGATACAGATATTGTGGGTGAGACTACCTATTA
CTTCAAGGCAATGACTTCTTCAAAAACTATGAAATTAAGAATGAAGTAGATAGGACCTTGACATATATAACTCTCCACAT
TTCTGAGTGCCTAAAGAAACTCCAGAAGCGCAATTCCAAAAACCAAGGCAAGAAAGAAACGTACACACTGGGAATCACTA
ACCTCCCCTTTCCTAGAGAGCCCAGTTTTCCACTTAATGACATTTATGCCAAACCAGCAAACGAACAAGAAGATGAAGTG
AGGAGGGTCTACTGACAGCAGCTACGGCAAGAGACAGGACTGAGACTCTGTGAGAAAGTTTTTGACCCACAGGATGGCAA
ACCCAGCAAGTGGTGGACTTGCTTTGTGAAGAGATAGCTGATGAACAAGAGTCTTTCAGGACCTGGA

ORF - retro_lafr_763 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.34 %
Parental protein coverage: 87.64 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLPIRSQFKGPAPRETKDTDIIDEAIYYFKA-NVFFKNYEIKNEADRTLIYITLYISECLKKLQKCNSKSQ
LPI....KG..P.ETKDTDI..E..YYFKA.N.FFKNYEIKNE.DRTL.YITL.ISECLKKLQK.NSK.Q
RetrocopyLPIKGLIKGRTP*ETKDTDIVGETTYYFKA<NDFFKNYEIKNEVDRTLTYITLHISECLKKLQKRNSKNQ
ParentalGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQETGLRLCEKVFDPLNDKPSKWW
G.KE.YTLGITN.P.P.EP.FPLN.IYAKPAN.QEDEV.R.Y.QQLRQETGLRLCEKVFDP...KPSKWW
RetrocopyGKKETYTLGITNLPFPREPSFPLNDIYAKPANEQEDEVRRVY*QQLRQETGLRLCEKVFDPQDGKPSKWW
ParentalTCFVKRQFMNKSLSGPG
TCFVKR..MNKSLSGPG
RetrocopyTCFVKR*LMNKSLSGPG

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_763 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 40 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000084561 retrocopy
Callithrix jacchus ENSCJAG000000093601 retrocopy
Dasypus novemcinctus ENSDNOG000000049872 retrocopies
Erinaceus europaeus ENSEEUG000000115312 retrocopies
Felis catus ENSFCAG000000041322 retrocopies
Loxodonta africana ENSLAFG00000006166 3 retrocopies
retro_lafr_1119, retro_lafr_763 , retro_lafr_840,
Macaca mulatta ENSMMUG000000064923 retrocopies
Monodelphis domestica ENSMODG000000116281 retrocopy
Nomascus leucogenys ENSNLEG000000028024 retrocopies
Oryctolagus cuniculus ENSOCUG000000119081 retrocopy
Otolemur garnettii ENSOGAG000000134241 retrocopy
Oreochromis niloticus ENSONIG000000037851 retrocopy
Procavia capensis ENSPCAG000000118582 retrocopies
Pongo abelii ENSPPYG000000049476 retrocopies
Sarcophilus harrisii ENSSHAG000000148053 retrocopies
Tarsius syrichta ENSTSYG000000029534 retrocopies
Tursiops truncatus ENSTTRG000000150832 retrocopies
Vicugna pacos ENSVPAG000000084041 retrocopy



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