RetrogeneDB ID:

retro_ptro_3043

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:GL392075.1:2230494..2230940(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CALM3
Ensembl ID:ENSPTRG00000006626
Aliases:None
Description:Pan troglodytes calmodulin 1 (phosphorylase kinase, delta) (CALM1), mRNA. [Source:RefSeq mRNA;Acc:NM_001110819]


Retrocopy-Parental alignment summary:






>retro_ptro_3043
ATGGCTGACCAACTGACTGAAAGGCAGATTGCAGAATTCAAAGAAACTTTTTCACTATTTAACAAAGATGGTGATGGAAC
TATAACAACAAGGAATCAGGAACTGTAATGAGGTCTCTTGGGCAGAATCCCACAGAAGCAGAGTTACAGGACATGATTAA
TGAAGTAGATGCTGATGGTAATGGCACAGTTGACTTCCCTGAATTTCTAACAATGATGGCAAGAAAAATGAAAGACACAG
ACAGTGAAGAAGAAATTAGAGATGCATTCTGTGTGTTTGATAAGGATGGCAATGGCTATATTAGTGCAACAGAACTTCAC
CATGTGACGACAAACCTTGGAGAGAATTTAACAGATGACGAGGTTGATGAAATGATCAGGTAACTAGATATTGATGTTGA
TGGTCAAATGATCTATGAAGAGTTAGTACAAATGATGACAGCAAAG

ORF - retro_ptro_3043 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.33 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMADQLTEEQIAEFKEAFSLFDKDGDGTITT-KELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEF
MADQLTE.QIAEFKE.FSLF.KDGDGTITT.KE.GTVMRSLGQNPTEAELQDMINEVDADGNGT.DFPEF
RetrocopyMADQLTERQIAEFKETFSLFNKDGDGTITT<KESGTVMRSLGQNPTEAELQDMINEVDADGNGTVDFPEF
ParentalLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNY
LTMMARKMKDTDSEEEIR.AF.VFDKDGNGYISA.EL.HV.TNLGE.LTD.EVDEMIR..DID.DGQ..Y
RetrocopyLTMMARKMKDTDSEEEIRDAFCVFDKDGNGYISATELHHVTTNLGENLTDDEVDEMIR*LDIDVDGQMIY
ParentalEEFVQMMTAK
EE.VQMMTAK
RetrocopyEELVQMMTAK

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .27 RPM 616 .72 RPM
SRP007412_cerebellum 0 .14 RPM 615 .63 RPM
SRP007412_heart 0 .03 RPM 192 .95 RPM
SRP007412_kidney 0 .10 RPM 216 .98 RPM
SRP007412_liver 0 .10 RPM 82 .03 RPM
SRP007412_testis 0 .63 RPM 100 .43 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_3043 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_3043 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3043 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1255
Gorilla gorilla retro_ggor_988
Pongo abelii retro_pabe_1045
Parental genes homology:
Parental genes homology involve 33 parental genes, and 74 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 ENSLAFG000000029051 retrocopy
retro_lafr_1165,
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 ENSPTRG00000006626 1 retrocopy
retro_ptro_3043 ,
Pan troglodytes ENSPTRG000000119014 retrocopies
retro_ptro_1195, retro_ptro_2623, retro_ptro_83, retro_ptro_881,
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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