RetrogeneDB ID:

retro_lafr_1165

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_8:66190570..66191086(+)
Located in intron of:ENSLAFG00000012963
Retrocopy
information
Ensembl ID:ENSLAFG00000025625
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CALM1
Ensembl ID:ENSLAFG00000002905
Aliases:None
Description:calmodulin 1 (phosphorylase kinase, delta) [Source:HGNC Symbol;Acc:1442]


Retrocopy-Parental alignment summary:






>retro_lafr_1165
AGGCATCCCTGCCATCACAGCCCATGTGCTGGGGCAGCCACCTTCGCTCCCTCTGTGGTTCCTCCATTCACCAGCACCAT
GGCTGAGCAGCTGACTGAAGAACAGATGGCTGAATTCAAGGAAGCTTTCTCCCTATTCCATGATGATGACGGCACCCTCA
CAACAAAGGAACTTGGAACTGCCATGAGGTCACTGGCTCAGAACCCAACAGAAGCTGAATTACAGGATACGATCAACAAG
GTGGACGCTGATGGTAATGGCACCATTGACTTCCCAGAGTTTTTGACTGTGATGGCTAGAAGAATGAAAGACACAGTGAA
GAAGAAATCTGTGAGGCATTCTGAGTCTGACAAGGATGGTAATGGTTATATCAGTGCAGCAGAACTACGTCGTGTCGTGA
CAAATTTAGGAGAAAAACTAACAATGAAGAGGTAGATGAAATGATCAGAGAAATAGACATTGATGGTGATGGACAAAGTC
AACCATGAAGAATTTGTACAGATAATGACTGCAAAA

ORF - retro_lafr_1165 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.62 %
Parental protein coverage: 89.74 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalRPPPPRLPPRGAFLALRSPPPGGRGAGADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNP
R.P....P..GA.....S..P......A.QLTEEQ.AEFKEAFSLF..D.DGT.TTKELGT.MRSL.QNP
RetrocopyRHPCHHSPCAGAATFAPSVVPPFTSTMAEQLTEEQMAEFKEAFSLFHDD-DGTLTTKELGTAMRSLAQNP
ParentalTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLG
TEAELQD.IN.VDADGNGTIDFPEFLT.MAR.MKDT......R......DKDGNGYISAAELR.V.TNLG
RetrocopyTEAELQDTINKVDADGNGTIDFPEFLTVMARRMKDTVKKKSVRHS--ESDKDGNGYISAAELRRVVTNLG
ParentalEKLT-DEEVDEMIREADIDGDGQ-VNYEEFVQMMTAK
EKLT..EEVDEMIRE.DIDGDGQ.VN.EEFVQ.MTAK
RetrocopyEKLT<NEEVDEMIREIDIDGDGQ>VNHEEFVQIMTAK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Loxodonta africana was not studied using ChIP-Seq data.

EST - click to see more details

Loxodonta africana was not studied using EST data.

TSS - click to see more details

Loxodonta africana was not studied using FANTOM5 data.

Lab - click to see more details

retro_lafr_1165 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 34 parental genes, and 76 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000157121 retrocopy
retro_acar_45,
Ailuropoda melanoleuca ENSAMEG000000018014 retrocopies
retro_amel_1215, retro_amel_1714, retro_amel_265, retro_amel_811,
Callithrix jacchus ENSCJAG000000177403 retrocopies
retro_cjac_1418, retro_cjac_2564, retro_cjac_693,
Dasypus novemcinctus ENSDNOG000000046459 retrocopies
retro_dnov_1093, retro_dnov_18, retro_dnov_1864, retro_dnov_1972, retro_dnov_2229, retro_dnov_241, retro_dnov_2522, retro_dnov_2674, retro_dnov_865,
Dipodomys ordii ENSDORG000000032006 retrocopies
retro_dord_108, retro_dord_113, retro_dord_201, retro_dord_212, retro_dord_29, retro_dord_5,
Equus caballus ENSECAG000000091621 retrocopy
retro_ecab_279,
Echinops telfairi ENSETEG000000093775 retrocopies
retro_etel_1062, retro_etel_1542, retro_etel_1812, retro_etel_587, retro_etel_854,
Homo sapiens ENSG000001986682 retrocopies
retro_hsap_1290, retro_hsap_3847,
Gallus gallus ENSGALG000000264451 retrocopy
retro_ggal_9,
Gorilla gorilla ENSGGOG000000285401 retrocopy
retro_ggor_2592,
Gadus morhua ENSGMOG000000093421 retrocopy
retro_gmor_23,
Latimeria chalumnae ENSLACG000000050591 retrocopy
retro_lcha_53,
Loxodonta africana ENSLAFG000000011555 retrocopies
retro_lafr_100, retro_lafr_156, retro_lafr_631, retro_lafr_646, retro_lafr_86,
Loxodonta africana ENSLAFG00000002905 1 retrocopy
retro_lafr_1165 ,
Loxodonta africana ENSLAFG000000098651 retrocopy
retro_lafr_655,
Meleagris gallopavo ENSMGAG000000130551 retrocopy
retro_mgal_13,
Microcebus murinus ENSMICG000000049803 retrocopies
retro_mmur_314, retro_mmur_35, retro_mmur_45,
Monodelphis domestica ENSMODG000000026964 retrocopies
retro_mdom_137, retro_mdom_178, retro_mdom_185, retro_mdom_208,
Monodelphis domestica ENSMODG000000092221 retrocopy
retro_mdom_1126,
Mustela putorius furoENSMPUG000000080871 retrocopy
retro_mputfur_523,
Mus musculus ENSMUSG000000011754 retrocopies
retro_mmus_1519, retro_mmus_2859, retro_mmus_2871, retro_mmus_50,
Nomascus leucogenys ENSNLEG000000170403 retrocopies
retro_nleu_2039, retro_nleu_2093, retro_nleu_2648,
Ornithorhynchus anatinus ENSOANG000000153651 retrocopy
retro_oana_9,
Oryctolagus cuniculus ENSOCUG000000116591 retrocopy
retro_ocun_626,
Otolemur garnettii ENSOGAG000000280891 retrocopy
retro_ogar_1727,
Petromyzon marinus ENSPMAG000000033231 retrocopy
retro_pmar_12,
Pongo abelii ENSPPYG000000060601 retrocopy
retro_pabe_1045,
Pelodiscus sinensis ENSPSIG000000131731 retrocopy
retro_psin_9,
Pan troglodytes ENSPTRG000000066261 retrocopy
retro_ptro_3043,
Pteropus vampyrus ENSPVAG000000100281 retrocopy
retro_pvam_1274,
Rattus norvegicus ENSRNOG000000040603 retrocopies
retro_rnor_318, retro_rnor_389, retro_rnor_392,
Sus scrofa ENSSSCG000000257683 retrocopies
retro_sscr_26, retro_sscr_390, retro_sscr_692,
Tursiops truncatus ENSTTRG000000135842 retrocopies
retro_ttru_1637, retro_ttru_1699,
Vicugna pacos ENSVPAG000000045631 retrocopy
retro_vpac_472,


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