RetrogeneDB ID:

retro_lafr_912

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_49:14485818..14486540(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SPIC
Ensembl ID:ENSLAFG00000015661
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_912
ACTTATATTGACGAAGACAAACTGGGTCAAGCATTTGAGGATGCTTTTCAGGTACAGAGGCAACATTCAACTGGCGATCC
TCCATACTCCCTAGACTTCAAAAATTACCTGGTTTTCATCAACCATTGCCTGCATGTCAGAGGAAGCTCCCATGACTATA
GAGGGTTGCCTACAGAGAAGCCTGTCTATACCTGGAGAACTGTAATCAACAGTGCTGCAGCTACTGTTTCGAAGGAAATA
TTCATCAATCTCTGCAGAGTATCACTGAAAACCAGCTAGTACCACCTGCTGTTCTCCAGCAAAAGGGAGGAAAAGGCAGG
AAGAAGCTCCCACTGTTTGAATACCTTTCATGAATCCCTCCGTAATCCCAAAAAGGCATCTTGTATTCAGTGGGTAGATA
TAACCAAAGGCATCTTTCAGTTTGTATCAGAAAAACACGGAAAGACACACAGAGCTTTGGGGAAAAAGAAAAGGCAACCG
GAAGACCCTGACTCACCAGAAAATAGCCAGAGCGCTGATGAATTATGGAAGAACTGGGAAAACCACCAAAAATCCAGAGA
AAGCTAGCTTACCAGTTCAGTGAGACCATTCTCCAGAGACTTTCTCCATGTTATTTCTTGGGGAAAGAGGTCTTCTACTC
ATAGTATGTCCAACGTGATCAAGAATATCTCAGCTTAAATAACTGGAACACAAGTTATAATCATACAGATGCCAATTACC
AT

ORF - retro_lafr_912 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.05 %
Parental protein coverage: 99.17 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalTCIEQDKLGQAFEDAFEVLRQHSAGDLQYSPDYKNYLAFINHCPHVRGNPNCYGMLPTEEPVYNWRTVIN
T.I..DKLGQAFEDAF.V.RQHS.GD..YS.D.KNYL.FINHC.HVRG....Y..LPTE.PVY.WRTVIN
RetrocopyTYIDEDKLGQAFEDAFQVQRQHSTGDPPYSLDFKNYLVFINHCLHVRGSSHDYRGLPTEKPVYTWRTVIN
ParentalSAA-DYYFEGNIHQSLQNIAESQLVQPAVLQQKGGKGRKKLRLFEYL-HESLCNPEMASCIQWVDKTKGI
SAA..Y.FEGNIHQSLQ.I.E.QLV.PAVLQQKGGKGRKKL.LFEYL.HESL.NP..ASCIQWVD.TKGI
RetrocopySAA<SYCFEGNIHQSLQSITENQLVPPAVLQQKGGKGRKKLPLFEYL>HESLRNPKKASCIQWVDITKGI
ParentalFQFVS-KNKERLAELWGKRKGNRKTMTYQKMARALRNYGRTGEIT-KIRRKLTYQFSEAILQRLSPSYFL
FQFVS.KN.ER..ELWGKRKGNRKT.T.QK.ARAL.NYGRTG..T.KI.RKL.YQFSE.ILQRLSP.YFL
RetrocopyFQFVS>KNTERHTELWGKRKGNRKTLTHQKIARALMNYGRTGKTT>KIQRKLAYQFSETILQRLSPCYFL
ParentalGKEIFYSQYIQPDQEYLSLNNWNASYNPMYANYH
GKE.FYS.Y.Q.DQEYLSLNNWN.SYN...ANYH
RetrocopyGKEVFYS*YVQRDQEYLSLNNWNTSYNHTDANYH

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_912 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 38 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000099042 retrocopies
Callithrix jacchus ENSCJAG000000019061 retrocopy
Dasypus novemcinctus ENSDNOG000000044961 retrocopy
Equus caballus ENSECAG000000096141 retrocopy
Echinops telfairi ENSETEG000000042176 retrocopies
Homo sapiens ENSG000001662114 retrocopies
Gorilla gorilla ENSGGOG000000245974 retrocopies
Loxodonta africana ENSLAFG00000015661 1 retrocopy
retro_lafr_912 ,
Myotis lucifugus ENSMLUG000000110521 retrocopy
Macaca mulatta ENSMMUG000000208731 retrocopy
Nomascus leucogenys ENSNLEG000000062321 retrocopy
Oryctolagus cuniculus ENSOCUG000000080701 retrocopy
Otolemur garnettii ENSOGAG000000151481 retrocopy
Pongo abelii ENSPPYG000000048734 retrocopies
Pan troglodytes ENSPTRG000000053514 retrocopies
Rattus norvegicus ENSRNOG000000057201 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000154573 retrocopies
Tursiops truncatus ENSTTRG000000172051 retrocopy



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