RetrogeneDB ID:

retro_lafr_1022

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_6:11313047..11313953(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MAPK3
Ensembl ID:ENSLAFG00000017904
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1022
GGCACAGTCAGCTCAGCTTATGACCACTTGCACAGGACTCGTGTGGTCATCAAGAAGATCAGCCCCTTAGAGCATCACAC
CACTTCCAGCACAAGCTTCCAGAGATCCAGATATTGCTACATTTCTGCCAGAAGAATGTTATCGGTATCCAAGACATTCT
GTAGGCAGCCACCCTGGGAGCCAGGAGGGATGTCTGCATTGTACAGGCCCCAATGGAGACAAACCTGTACAAGTTGCTCA
AAAGCTGACAGCTGGGAAATGACCATGTCCACTATTTCCTCTACCAGATCCTGTGGGGCCTCAAGTATATTTGCTCAGCC
AACATGCTGCTTGGAAACCTAAGGCCCTCCAACTTGCTCATCAACACCACCTGTGACCTTAAAATCTGTGATTTCAGCCT
GGCCCAGATCCCTGATCCTGAACAGGACCACACCGGCTTTTTGACAGAGTACGTAGCTACACACTGGTACTGGGCACCAG
AGATCAAGCTCAACTCCAAGAGCTATACCCAATCTATTGACACCTGATCTGTGGGTTGCATCCTGGCTGAGATGCTCTCC
AACCAGCCCATCTTCCCCGGCAAGCACTACTTGGATCAGCTTAACTAAATTCTGAGTGTTCTGGGCTCCCCATCCTAAGA
GGACCTGAATTGTATCATCAACATGAAGGCTTGAAGCTACCTAGAATCGCTGCCCACCAAGACCAAGGTGGCCTTGGCCA
AGCTCTTTCCCAAGTCAGACCCCAAAGCCCCTAAACAGGATGTTGACCTTTAACTCCAACAAACAGATCACAGTGGAAGA
AGCATTGGCCCACCCCTACCTGGAGCAGTACTATCACCCCATGGATAAGCTGGTGGCTGATGAAACCTTTGCCTTTAACA
TGGAATTAGATGATCTACCAAAGGAA

ORF - retro_lafr_1022 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.92 %
Parental protein coverage: 93.56 %
Number of stop codons detected: 6
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGPLSSAYDHVRKIRVAIKKISPFEHQT-YCQRTLREIQILLRFRHENVIGIRDILRAPTLEAMRDVYIVQ
G..SSAYDH....RV.IKKISP.EH.T...Q..L.EIQILL.F...NVIGI.DIL.A.TL.A.RDV.IVQ
RetrocopyGTVSSAYDHLHRTRVVIKKISPLEHHT<HFQHKLPEIQILLHFCQKNVIGIQDIL*AATLGARRDVCIVQ
ParentalDLMETDLYKLLKSQQLSNDHVCYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIAD
..MET.LYKLLKS.QL.NDHV.YFLYQIL.GLKYI.SAN.L...L.PSNLLINTTCDLKICDF.LA.I.D
RetrocopyAPMETNLYKLLKS*QLGNDHVHYFLYQILWGLKYICSANMLLGNLRPSNLLINTTCDLKICDFSLAQIPD
ParentalPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILSILG
PE.DHTGFLTEYVAT.WY.APEI.LNSK.YT.SID..SVGCILAEMLSN.PIFPGKHYLDQLN.ILS.LG
RetrocopyPEQDHTGFLTEYVATHWYWAPEIKLNSKSYTQSIDT*SVGCILAEMLSNQPIFPGKHYLDQLN*ILSVLG
ParentalSPSQEDLNCIINMKARNYLQSLPAKTKVAWAKLF-PKSDPKALELLDRMLTFNPNKRITVEEALAHPYLE
SPS.EDLNCIINMKA..YL.SLP.KTKVA.AKLF.P...PK....L.RMLTFN.NK.ITVEEALAHPYLE
RetrocopySPS*EDLNCIINMKA*SYLESLPTKTKVALAKLF>PSQTPKP---LNRMLTFNSNKQITVEEALAHPYLE
ParentalQYYDPTDEPVAEEPFTFDMELDDLPKE
QYY.P.D..VA.E.F.F.MELDDLPKE
RetrocopyQYYHPMDKLVADETFAFNMELDDLPKE

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_1022 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 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000171081 retrocopy
Dasypus novemcinctus ENSDNOG000000021911 retrocopy
Loxodonta africana ENSLAFG00000017904 1 retrocopy
retro_lafr_1022 ,
Myotis lucifugus ENSMLUG000000112841 retrocopy
Mus musculus ENSMUSG000000630651 retrocopy
Pongo abelii ENSPPYG000000072391 retrocopy
Rattus norvegicus ENSRNOG000000196011 retrocopy



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