RetrogeneDB ID:

retro_lafr_1062

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_63:10465166..10465438(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HBXIP
Ensembl ID:ENSLAFG00000012907
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1062
TTGGACACAACCTTGAAGCAGCACTTGGGGGACACAATGAAGAATTCTTCCATTGTTGGAGTCCTGTGCGCAGATTCACA
AGGACTCAATCTGGGCTGCTGTGGAACCCTGTCAGATAGCATGCTGGGGTGATATATGTTCTAGCCTGGCAAACAGCTAA
GCTGACCTCTGACCCCACTGCTATTCCTGTGGTGCGTCTAGAATCAGGTAACAGGAACATTAGGATCCAGGAACCCAATA
ACCCCACAGTGGCAGTGCACAAAATGGCCTCT

ORF - retro_lafr_1062 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.91 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMETTLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDE-HAGVISVLAQQAAKLTSDPTDIPVVCLES
..TTL.QHL.DTMKN.SIVGVLC.DSQGLNLGC.GTLSD..HAGVI.VLA.Q.AKLTSDPT.IPVV.LES
RetrocopyLDTTLKQHLGDTMKNSSIVGVLCADSQGLNLGCCGTLSDS<HAGVIYVLAWQTAKLTSDPTAIPVVRLES
ParentalDSGNVMIQKHDGITVAVHKMAS
...N..IQ.....TVAVHKMAS
RetrocopyGNRNIRIQEPNNPTVAVHKMAS

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_1062 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 6 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000115042 retrocopies
Bos taurus ENSBTAG000000149703 retrocopies
Loxodonta africana ENSLAFG00000012907 5 retrocopies
Macaca mulatta ENSMMUG000000150234 retrocopies
Sus scrofa ENSSSCG000000068071 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000034015 retrocopies



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