RetrogeneDB ID:

retro_lafr_795

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_39:13967181..13967764(+)
Located in intron of:ENSLAFG00000017062
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHP1
Ensembl ID:ENSLAFG00000014743
Aliases:None
Description:calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]


Retrocopy-Parental alignment summary:






>retro_lafr_795
ATGGGGTCTCAGACCTCCACATTACTGCAGGAGGAAGAGCTCGAGGAAGTCAAGCAGGAGACTGGCTTTTCCCACAATCA
GATTCATCCGAATCTATGGGCGGTTCACTAGTCTGGACTGAGGAGAGAATGGGACTCTCAGCTGGGAAGACTTCCAGCAG
ATTCCAGATCTTGTCATCAACCCATTGGGGGACCGTATCATCAGTGCCTTCTTTCCAGAAGGAGAGGACCAGGTCAACTT
CCGTGGATTCATAAGAACTTTGGCTTATTTCAGACCCACTGGCTGTAGTGAAGACAGCAAAGATGTGAATGGGCCAGAAC
CAATCAACAGCAGAATGAACAAACTGCACTTTGCTTTCAAATTATATGATTTGGATAAAGATGGCAAGATCTCCCATGAT
GAGCTGTTACAGGTGCTATGCATGATGGCTGGAGTGAATATCTTGGAAGAGCAGCTTGGGAGCATCACAGACAGGACCAT
CCAGGAGACCAATCTGGATGGGGATGGCGCCATATCTTTCTCAGAATTTGTTAAGGTTTTGGAAAAGGTTGACGTAGAAC
AGAGAATGAGCATTCACTTTCTT

ORF - retro_lafr_795 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.97 %
Parental protein coverage: 99.49 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGSRASTLLRDEELEEIKKETGFSHSQI-TRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINA
MGS..STLL..EELEE.K.ETGFSH.QI..R.Y.RFTSLD.GENGTLS.EDFQ.IP.L.INPLGDRII.A
RetrocopyMGSQTSTLLQEEELEEVKQETGFSHNQI>IRIYGRFTSLD*GENGTLSWEDFQQIPDLVINPLGDRIISA
ParentalFFPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVL
FFPEGEDQVNFRGF.RTLA.FRP....E.SKDVNGPEP.NSR.NKLHFAF.LYDLDKD.KIS.DELLQVL
RetrocopyFFPEGEDQVNFRGFIRTLAYFRPTGCSEDSKDVNGPEPINSRMNKLHFAFKLYDLDKDGKISHDELLQVL
ParentalRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFL
.MM.GVNI..EQLGSI.DRTIQE...DGD.AISF.EFVKVLEKVDVEQ.MSI.FL
RetrocopyCMMAGVNILEEQLGSITDRTIQETNLDGDGAISFSEFVKVLEKVDVEQRMSIHFL

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_795 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 12 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000271731 retrocopy
Callithrix jacchus ENSCJAG000000207611 retrocopy
Equus caballus ENSECAG000000197511 retrocopy
Felis catus ENSFCAG000000063461 retrocopy
Gorilla gorilla ENSGGOG000000073122 retrocopies
Loxodonta africana ENSLAFG00000014743 3 retrocopies
retro_lafr_221, retro_lafr_795 , retro_lafr_838,
Loxodonta africana ENSLAFG000000226821 retrocopy
Oryctolagus cuniculus ENSOCUG000000138321 retrocopy
Otolemur garnettii ENSOGAG000000130992 retrocopies
Procavia capensis ENSPCAG000000054191 retrocopy
Pongo abelii ENSPPYG000000063702 retrocopies
Pteropus vampyrus ENSPVAG000000031501 retrocopy



Copyright © RetrogeneDB 2014-2017