RetrogeneDB ID:

retro_sscr_390

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:13:155540344..155540791(-)
Located in intron of:ENSSSCG00000011913
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CALM1
Ensembl ID:ENSSSCG00000025768
Aliases:None
Description:Sus scrofa calmodulin 1 (CALM1), mRNA. [Source:RefSeq mRNA;Acc:NM_001244210]


Retrocopy-Parental alignment summary:






>retro_sscr_390
ATGGCTGACCAACTGACTGAAGAGCAGATCGCAGAATTCAAAGAAGCTTTTTCACTATTTGACAAGGATGGTGATGGAAC
TATAACAACAAAGGAATTGGTAACTGTACTGAGGTCTCTTGGGCAGAATCTCACAGAAGCAGAGTTACAGGACATGATTC
ATGAAGTAGATGTTGATAGTAATGGCGAAACTGACTTCCTGGAATTTCTGACAATGATGGCAAGAAAAATGAAAGACACA
GACAGTGAAGAAGAAATTAGAGAAGCATTCCATGTGTTTGAAAAGGATGACAATAGCTATATTAGTGCAGCAGAGCTTCA
CCATGTGATGACAAACCTTGGAGAGAAGTTAACAGATGAAGAGGTTGATGAAATGATCAAGGAAGCAGATAGTGATGGTG
ATGGTCAAGTAGACCATGAAGAGCTTGTAAAAATGATGACAGCAAAA

ORF - retro_sscr_390 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.58 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKEL.TV.RSLGQN.TEAELQDMI.EVD.D.NG..DF.EFL
RetrocopyMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELVTVLRSLGQNLTEAELQDMIHEVDVDSNGETDFLEFL
ParentalTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
TMMARKMKDTDSEEEIREAF.VF.KD.N.YISAAEL.HVMTNLGEKLTDEEVDEMI.EAD.DGDGQV..E
RetrocopyTMMARKMKDTDSEEEIREAFHVFEKDDNSYISAAELHHVMTNLGEKLTDEEVDEMIKEADSDGDGQVDHE
ParentalEFVQMMTAK
E.V.MMTAK
RetrocopyELVKMMTAK

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
SRP014902_placenta 0 .00 RPM 171 .22 RPM
SRP014902_testis 0 .14 RPM 72 .42 RPM
SRP018288_heart 0 .05 RPM 173 .43 RPM
SRP018288_kidney 0 .59 RPM 139 .39 RPM
SRP018288_liver 0 .16 RPM 56 .93 RPM
SRP018288_lung 0 .00 RPM 192 .45 RPM
SRP018856_adipose 0 .05 RPM 205 .37 RPM
SRP035408_brain 2 .10 RPM 1287 .25 RPM
SRP035408_liver 0 .62 RPM 60 .06 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_sscr_390 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_390 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_390 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 31 parental genes, and 69 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 ENSPTRG000000066261 retrocopy
retro_ptro_3043,
Rattus norvegicus ENSRNOG000000040603 retrocopies
retro_rnor_318, retro_rnor_389, retro_rnor_392,
Sus scrofa ENSSSCG000000084331 retrocopy
retro_sscr_228,
Sus scrofa ENSSSCG00000025768 3 retrocopies
retro_sscr_26, retro_sscr_390 , retro_sscr_692,
Tursiops truncatus ENSTTRG000000135842 retrocopies
retro_ttru_1637, retro_ttru_1699,




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