RetrogeneDB ID:

retro_lafr_400

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_147:854294..854779(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SSU72
Ensembl ID:ENSLAFG00000002076
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_400
ATGCCCTCATCTCCACTCAGGCTGGCTGTGGTGTATATCAGTAACATCAACTGGAGCATGGAAGTCCACAGTATCCTCAG
GAAAAAGGGGTTCAGTGTCTAGTCTTTTGGGACTAGACCTCATGTGAAACTCCCAGAGCCAGGACCCAATCTCTCCTTGG
TTTACGATTTTGCAACAACATATCAACAAATGTACAAGGATCTTGTAAGGAAAGACAGAGAATACTATACCCATAATGGA
ATGTTACACATCTTGGGAAGAAATCAGAGGATCAAGCCCCAGCCGGAAAGATTTCAAGAGTGCAGAGATGCCTTCGAAGT
CATCATAACCTGTGACGAGACGGTCTATGACAGAGTGGTGGAAGAGCTGTGTTCCAGAGAACAAGAGACCTTCCAGGCCA
CACATGTGATCAATGTGGACAATGAAGACACCCTGGAAGACACCACCCTGGGATTTTCCTCATTTGTAAGCTCTGCCAGC
ACATA

ORF - retro_lafr_400 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.87 %
Parental protein coverage: 83.51 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPSSPLRVAVVCSSNQNRSMEAHNILSKRGFSVRSFGTGTHVKLPGPAPDKPNVYDFKTTYDQMYNDLLR
MPSSPLR.AVV..SN.N.SME.H.IL.K.GFSV.SFGT..HVKLP.P.P....VYDF.TTY.QMY.DL.R
RetrocopyMPSSPLRLAVVYISNINWSMEVHSILRKKGFSV*SFGTRPHVKLPEPGPNLSLVYDFATTYQQMYKDLVR
ParentalKDKELYTQNGILHMLDRNKRIKPRPERFQNCKDLFDLILTCEERVYDQVVEDLNSREQETCQPVHVINVD
KD.E.YT.NG.LH.L.RN.RIKP.PERFQ.C.D.F..I.TC.E.VYD.VVE.L.SREQET.Q..HVINVD
RetrocopyKDREYYTHNGMLHILGRNQRIKPQPERFQECRDAFEVIITCDETVYDRVVEELCSREQETFQATHVINVD
ParentalIQDNHEEATL-GAFLICELCQCI
..D..E..TL.G.FLIC.LCQ.I
RetrocopyNEDTLEDTTL<GIFLICKLCQHI

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_400 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 22 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137363 retrocopies
Canis familiaris ENSCAFG000000192542 retrocopies
Callithrix jacchus ENSCJAG000000109573 retrocopies
Cavia porcellus ENSCPOG000000022382 retrocopies
Dipodomys ordii ENSDORG000000117141 retrocopy
Homo sapiens ENSG000001600758 retrocopies
Gorilla gorilla ENSGGOG000000044211 retrocopy
Loxodonta africana ENSLAFG00000002076 4 retrocopies
Macropus eugenii ENSMEUG000000151701 retrocopy
Myotis lucifugus ENSMLUG000000165172 retrocopies
Macaca mulatta ENSMMUG000000015511 retrocopy
Monodelphis domestica ENSMODG000000066163 retrocopies
Mustela putorius furoENSMPUG000000143942 retrocopies
Mus musculus ENSMUSG000000290381 retrocopy
Otolemur garnettii ENSOGAG000000244302 retrocopies
Pongo abelii ENSPPYG000000020001 retrocopy
Pan troglodytes ENSPTRG0000000003416 retrocopies
Pteropus vampyrus ENSPVAG000000176954 retrocopies
Rattus norvegicus ENSRNOG000000178292 retrocopies
Sus scrofa ENSSSCG000000033482 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000029604 retrocopies
Tursiops truncatus ENSTTRG000000170512 retrocopies



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