RetrogeneDB ID:

retro_lafr_931

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_5:99571075..99571643(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MED27
Ensembl ID:ENSLAFG00000011556
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_931
GTGGATCCTGTGCAGGACAAAACTCCTCTCTGTAGTCAGCTCCTTCAAGCATATAAATGGTCAAACAAGTTGCAGTACCA
CGCAGGTCTAGCATCTGGCCTTTTGAATTGACAGTTGTTGAAACATTCTGCTAACCATGTGGGAGTATCTGCTAAACAGA
CAAAAGGCTCAACCCGCGACTCTTGTCTTACCTCCTCAGTATGTTGATGATGTGATCAGCCACACTGACAAGATGTTTCC
TGAAGTGTCAGTCCACTTACCCAGACCCAATGGAACCTCAGCAATGCATCTGGTGACTTTGGGAAAGGTGTTGAAAGTGA
TTGTCATCATGTGGAGCGTATTCATTGATGGAACAATGGTAAAGGGATATAACAAAAATGTTTACAAAGATGGCAAGCTT
GATGTATGGTCCAAATCTAACTATCAAGTGTTCCAAAAGGTGACAGACCATGCCACTAGTGCCGTGCTTCACTATCAGTT
GTCCCAGATTCCAGACGTCGTGGTCAGATCCTTCATGACCTGGTTAAGAAGTTACATAAAGCTGTTTCAGGCCCCATGCC
AACGCTGC

ORF - retro_lafr_931 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.69 %
Parental protein coverage: 61.41 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLDPVQDKTPLYSQLLQAYKWSNKLQYHAGLASGLLNQQSLKRSANQMGVSAK-RRPKAQPTTLVLPPQYV
.DPVQDKTPL.SQLLQAYKWSNKLQYHAGLASGLLN.Q.LK.SAN..GVSAK.R......T....P.QYV
RetrocopyVDPVQDKTPLCSQLLQAYKWSNKLQYHAGLASGLLN*QLLKHSANHVGVSAK>RQKAQPATLVLPP-QYV
ParentalDDVISRIDRMFPEMSIHLSRPNGTSAMLLVTLGKVLKVIVVMRSLFIDRTIVKGYNENVYTEDGKLDIWS
DDVIS..D.MFPE.S.HL.RPNGTSAM.LVTLGKVLKVIV.M.S.FID.T.VKGYN.NVY..DGKLD.WS
RetrocopyDDVISHTDKMFPEVSVHLPRPNGTSAMHLVTLGKVLKVIVIMWSVFIDGTMVKGYNKNVY-KDGKLDVWS
ParentalKSNYQVFQKVTDHATTALLHYQLPQMPDVVVRSFMTWLRSYIKLFQAPCQRC
KSNYQVFQKVTDHAT.A.LHYQL.Q.PDVVVRSFMTWLRSYIKLFQAPCQRC
RetrocopyKSNYQVFQKVTDHATSAVLHYQLSQIPDVVVRSFMTWLRSYIKLFQAPCQRC

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_931 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
Homo sapiens ENSG000001605631 retrocopy
Gorilla gorilla ENSGGOG000000103901 retrocopy
Loxodonta africana ENSLAFG00000011556 1 retrocopy
retro_lafr_931 ,
Myotis lucifugus ENSMLUG000000003641 retrocopy
Nomascus leucogenys ENSNLEG000000128281 retrocopy
Pongo abelii ENSPPYG000000197061 retrocopy
Pan troglodytes ENSPTRG000000214921 retrocopy



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