RetrogeneDB ID:

retro_lafr_184

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_1:48184220..48184689(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL29
Ensembl ID:ENSLAFG00000005757
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_184
ATGGCCAAGACCAAGAACCATACCATGCATAACCAATCCCTAAAATGGCACAGAATTGGCATCAAGAAACCTTGATTCCA
ACGATATGATTTTCTTAAGGGGGTGAACCCCAAGTTCCTGAGGAACATGTGCTTTGCCAAGTAGCAAAACAAGAAGGGCC
TGAAGAAGATGCAGGCCAACAATGCCAAAGCCATGGATGCACATGCTGAGGCTATCAAGACTCTCTTAAGGCCTAAGGAG
GTCAAACCCAAGAACCCAAGGGGTGTCAACTGCAAGCTCAGTCAACTGGCCTACATTGCCCACTCCAAGCTTGGAAAGCA
TGCTTGGGACCACATTGCCAAAGGTCTCAGGCTCTGCTGGCCAAAGTCCAAACCAAGGCTGTAAGTAAGGCCAAGCTTCA
GCCAAGTCCTCAATACAAGTTTTGGTTCCAGGTCAGGCTCCCAAAGGTGCCCAGGCCCCCTCAAAGTCT

ORF - retro_lafr_184 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.47 %
Parental protein coverage: 95.73 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNKKGLKKMQANNAKAMDARTE
MAK.KNHT.HNQS.KWHR.GIKKP..QRY..LKGV.PKFLRNM.FAK..NKKGLKKMQANNAKAMDA..E
RetrocopyMAKTKNHTMHNQSLKWHRIGIKKP*FQRYDFLKGVNPKFLRNMCFAK*QNKKGLKKMQANNAKAMDAHAE
ParentalAIKTLLKPKQVKPKIPRGVNRKLSRLAYIAHPKLGKRARARIAKGLRLCRPKSK-AKAQSKA-EAPAQAS
AIKTLL.PK.VKPK.PRGVN.KLS.LAYIAH.KLGK.A...IAKGLRLC.PKSK..KA.SKA..A.A..S
RetrocopyAIKTLLRPKEVKPKNPRGVNCKLSQLAYIAHSKLGKHAWDHIAKGLRLCWPKSK<TKAVSKA<QASAKSS
ParentalIQDPAPAQAPKGAQAPTKA
IQ...P.QAPKGAQAP.K.
RetrocopyIQVLVPGQAPKGAQAPSKS

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_184 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 162 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091636 retrocopies
Callithrix jacchus ENSCJAG000000059519 retrocopies
Felis catus ENSFCAG000000017629 retrocopies
Gorilla gorilla ENSGGOG0000002469116 retrocopies
Loxodonta africana ENSLAFG00000005757 5 retrocopies
Microcebus murinus ENSMICG000000027059 retrocopies
Myotis lucifugus ENSMLUG0000001508814 retrocopies
Macaca mulatta ENSMMUG000000192482 retrocopies
Monodelphis domestica ENSMODG0000002875017 retrocopies
Mustela putorius furoENSMPUG000000117346 retrocopies
Mus musculus ENSMUSG000000487583 retrocopies
Otolemur garnettii ENSOGAG000000137662 retrocopies
Procavia capensis ENSPCAG000000097124 retrocopies
Pongo abelii ENSPPYG0000001381821 retrocopies
Rattus norvegicus ENSRNOG0000001113815 retrocopies
Sorex araneus ENSSARG000000135728 retrocopies
Sarcophilus harrisii ENSSHAG000000068542 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000002048814 retrocopies



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