RetrogeneDB ID:

retro_ptro_83

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:10:5603398..5603848(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000002256
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CALM3
Ensembl ID:ENSPTRG00000011901
Aliases:None
Description:Pan troglodytes calmodulin 2 (phosphorylase kinase, delta) (CALM2), mRNA. [Source:RefSeq mRNA;Acc:NM_001098558]


Retrocopy-Parental alignment summary:






>retro_ptro_83
ATGGCCGACCAGCTGACTGAGGAGCAGGTCACAGAATTCAAGGAGGCCTTCTCCCTGTTTGACAAGGATGGGGACGGCTG
CATCACCACCCGCGAGCTGGGCACGGTCATGCGGTCCCTGGGCCAGAACCCCACGGAGGCCGAGCTGCGGGACATGATGA
GTGAGATCGACCGGGACGGCAACGGCACCGTGGACTTCCCCGAGTTCCTGGGCATGATGGCCAGGAAGATGAAGGACACG
GACAACGAGGAGGAGATCCGCGAGGCCTTCCGCGTGTTCGACAAGGACGGCAACGGCTTCGTCAGCGCCGCCGAGCTGCG
ACACGTCATGACCCGGCTGGGGGAGAAGCTGAGTGACGAGGAGGTGGACGAGATGATCCGGGCCGCGGACACGGACGGAG
ACGGACAGGTGAACTACGAGGAGTTTGTCCGTGTGCTGGTGTCCAAGTGA

ORF - retro_ptro_83 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.56 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL
MADQLTEEQ..EFKEAFSLFDKDGDG.ITT.ELGTVMRSLGQNPTEAEL.DM..E.D.DGNGT.DFPEFL
RetrocopyMADQLTEEQVTEFKEAFSLFDKDGDGCITTRELGTVMRSLGQNPTEAELRDMMSEIDRDGNGTVDFPEFL
ParentalTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
.MMARKMKDTD.EEEIREAFRVFDKDGNG..SAAELRHVMT.LGEKL.DEEVDEMIR.AD.DGDGQVNYE
RetrocopyGMMARKMKDTDNEEEIREAFRVFDKDGNGFVSAAELRHVMTRLGEKLSDEEVDEMIRAADTDGDGQVNYE
ParentalEFVQMMTAK
EFV.....K
RetrocopyEFVRVLVSK

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 .43 RPM 332 .61 RPM
SRP007412_cerebellum 0 .18 RPM 318 .69 RPM
SRP007412_heart 0 .00 RPM 117 .11 RPM
SRP007412_kidney 32 .45 RPM 119 .41 RPM
SRP007412_liver 0 .43 RPM 91 .85 RPM
SRP007412_testis 0 .74 RPM 783 .52 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_83 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_83 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_83 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_59
Gorilla gorilla retro_ggor_187
Pongo abelii retro_pabe_45
Mus musculus retro_mmus_50
Rattus norvegicus retro_rnor_318
Equus caballus retro_ecab_59
Parental genes homology:
Parental genes homology involve 31 parental genes, and 107 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000157121 retrocopy
retro_acar_45,
Ailuropoda melanoleuca ENSAMEG000000062042 retrocopies
retro_amel_63, retro_amel_72,
Choloepus hoffmanni ENSCHOG000000082456 retrocopies
retro_chof_1940, retro_chof_2261, retro_chof_367, retro_chof_735, retro_chof_833, retro_chof_965,
Callithrix jacchus ENSCJAG000000006384 retrocopies
retro_cjac_1039, retro_cjac_1401, retro_cjac_2859, retro_cjac_4097,
Cavia porcellus ENSCPOG000000121813 retrocopies
retro_cpor_1012, retro_cpor_87, retro_cpor_89,
Equus caballus ENSECAG000000083964 retrocopies
retro_ecab_15, retro_ecab_59, retro_ecab_750, retro_ecab_882,
Echinops telfairi ENSETEG000000093775 retrocopies
retro_etel_1062, retro_etel_1542, retro_etel_1812, retro_etel_587, retro_etel_854,
Ficedula albicollis ENSFALG000000128281 retrocopy
retro_falb_16,
Felis catus ENSFCAG000000291415 retrocopies
retro_fcat_1926, retro_fcat_591, retro_fcat_629, retro_fcat_87, retro_fcat_88,
Gadus morhua ENSGMOG000000093421 retrocopy
retro_gmor_23,
Latimeria chalumnae ENSLACG000000050591 retrocopy
retro_lcha_53,
Loxodonta africana ENSLAFG000000098651 retrocopy
retro_lafr_655,
Myotis lucifugus ENSMLUG000000290166 retrocopies
retro_mluc_13, retro_mluc_1732, retro_mluc_18, retro_mluc_19, retro_mluc_2207, retro_mluc_2258,
Macaca mulatta ENSMMUG000000174661 retrocopy
retro_mmul_256,
Monodelphis domestica ENSMODG000000092221 retrocopy
retro_mdom_1126,
Mustela putorius furoENSMPUG000000120614 retrocopies
retro_mputfur_1207, retro_mputfur_21, retro_mputfur_838, retro_mputfur_942,
Oryctolagus cuniculus ENSOCUG000000021072 retrocopies
retro_ocun_1468, retro_ocun_84,
Otolemur garnettii ENSOGAG000000088246 retrocopies
retro_ogar_1126, retro_ogar_1196, retro_ogar_1432, retro_ogar_1535, retro_ogar_209, retro_ogar_2326,
Ochotona princeps ENSOPRG000000154787 retrocopies
retro_opri_1129, retro_opri_1155, retro_opri_16, retro_opri_40, retro_opri_506, retro_opri_830, retro_opri_86,
Petromyzon marinus ENSPMAG000000033231 retrocopy
retro_pmar_12,
Pongo abelii ENSPPYG000000124305 retrocopies
retro_pabe_1068, retro_pabe_1133, retro_pabe_115, retro_pabe_45, retro_pabe_599,
Pelodiscus sinensis ENSPSIG000000131731 retrocopy
retro_psin_9,
Pan troglodytes ENSPTRG000000066261 retrocopy
retro_ptro_3043,
Pan troglodytes ENSPTRG00000011901 4 retrocopies
retro_ptro_1195, retro_ptro_2623, retro_ptro_83 , retro_ptro_881,
Pteropus vampyrus ENSPVAG000000051832 retrocopies
retro_pvam_558, retro_pvam_560,
Sorex araneus ENSSARG000000087311 retrocopy
retro_sara_119,
Sus scrofa ENSSSCG000000084331 retrocopy
retro_sscr_228,
Ictidomys tridecemlineatus ENSSTOG000000218147 retrocopies
retro_itri_1048, retro_itri_1473, retro_itri_37, retro_itri_433, retro_itri_68, retro_itri_778, retro_itri_859,
Tupaia belangeri ENSTBEG0000000056917 retrocopies
retro_tbel_1450, retro_tbel_24, retro_tbel_2418, retro_tbel_258, retro_tbel_2612, retro_tbel_2856, retro_tbel_2933, retro_tbel_3150, retro_tbel_3195, retro_tbel_3956, retro_tbel_4141, retro_tbel_4171, retro_tbel_4212, retro_tbel_4324, retro_tbel_675, retro_tbel_722, retro_tbel_765,
Taeniopygia guttata ENSTGUG000000025811 retrocopy
retro_tgut_6,
Tarsius syrichta ENSTSYG000000125645 retrocopies
retro_tsyr_1641, retro_tsyr_2012, retro_tsyr_2128, retro_tsyr_2148, retro_tsyr_576,


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