RetrogeneDB ID:

retro_lafr_1237

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_9:75844512..75844759(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS21
Ensembl ID:ENSLAFG00000015793
Aliases:None
Description:40S ribosomal protein S21 [Source:UniProtKB/TrEMBL;Acc:G3TFU7]


Retrocopy-Parental alignment summary:






>retro_lafr_1237
GTGCAGAATAACGCCAGCAAGTTCGTGGACCTGGATGTGTCACGTAAATGCTCCACCAGCAACTGCATCATGACCACCAA
GGACCACGCATTCATCCAGATGAACGTGGCTGAGCTTGACAAGGTCACTGTCAGGTTCAACGGCCTATGAAGACCTACGC
TATCTACAGGGTCATTCACAGGATGGTGAGTCAGATGATTCTATTCTCTGACTGGCCAAGGCCGACGGCATTGTCTCAGA
GAACTTC

ORF - retro_lafr_1237 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.76 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNG-QFKTYAICGAIRRM-GESDDS
.QN.A..FVDL.V.RKCS.SN.I...KDHA.IQMNVAE.DKVT.RFNG...KTYAI...I.RM.GESDDS
RetrocopyVQNNASKFVDLDVSRKCSTSNCIMTTKDHAFIQMNVAELDKVTVRFNG<PMKTYAIYRVIHRM<GESDDS
ParentalILRLAKADGIVSKNF
IL.LAKADGIVS.NF
RetrocopyIL*LAKADGIVSENF

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_1237 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 20 parental genes, and 73 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000173992 retrocopies
Bos taurus ENSBTAG000000207952 retrocopies
Canis familiaris ENSCAFG000000126764 retrocopies
Callithrix jacchus ENSCJAG000000141955 retrocopies
Erinaceus europaeus ENSEEUG000000045732 retrocopies
Gorilla gorilla ENSGGOG000000237457 retrocopies
Latimeria chalumnae ENSLACG000000127531 retrocopy
Loxodonta africana ENSLAFG00000015793 4 retrocopies
Macropus eugenii ENSMEUG000000158322 retrocopies
Microcebus murinus ENSMICG000000129975 retrocopies
Macaca mulatta ENSMMUG000000050068 retrocopies
Ochotona princeps ENSOPRG000000009371 retrocopy
Pongo abelii ENSPPYG000000112058 retrocopies
Pan troglodytes ENSPTRG000000137081 retrocopy
Pteropus vampyrus ENSPVAG000000035482 retrocopies
Rattus norvegicus ENSRNOG000000063252 retrocopies
Sus scrofa ENSSSCG000000218251 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000010295 retrocopies
Tarsius syrichta ENSTSYG000000070615 retrocopies
Tursiops truncatus ENSTTRG000000111056 retrocopies



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