RetrogeneDB ID:

retro_sscr_57

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:GL892891.1:45376..45895(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSSCG00000028613
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CETN2
Ensembl ID:ENSSSCG00000012757
Aliases:None
Description:centrin, EF-hand protein, 2 [Source:HGNC Symbol;Acc:1867]


Retrocopy-Parental alignment summary:






>retro_sscr_57
ATGGCTTCCAGCTTCAAGAAGCCACAAGTGGCCTCCACCAGCCAGAAAAGAAAGGTGGGCCCTAAGCCTGAACTCACTGA
AGATCAGAAGCAAGAAGTTCGCGAAGCGTTTGACCTCTTCGATGCTGACGGCAGCGGCACCATCGACGTGAAGGAGCTGA
AGGTGGCTATGCGAGCGCTGGGCTTTGAACCCAGAAAGGAGGAGATGAAGAGGATGATCTCGGAGGTGGACAAGGAAGGC
ACAGGGAAAATCAGCTTCAATGACTTCCTGGCCGTGATGACGCAGAAGATGGCCGAGAAGGATACCAAAGAGGAAATCCT
GAAGGCTTTCAGGCTCTTTGACGACGATGAAACTGGCAAGATCTCATTCAAAAATCTAAAACGCGTGGCCAACGAGTTGG
GGGAAAACCTCACGGATGAGGAGCTTCAGGAAATGATTGACGAAGCGGACCGGGATGGAGACGGCGAAGTGAACGAGGAA
GAATTTCTTCGGATCATGAAAAAGACCAACCTTTATTAA

ORF - retro_sscr_57 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.88 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMASNFKKTNVASAAQRKRMSPKPELTEEQKQEIREAFDLFDADGTGTIDVKELKVAMRALGFEPKKEEIK
MAS.FKK..VAS..Q.....PKPELTE.QKQE.REAFDLFDADG.GTIDVKELKVAMRALGFEP.KEE.K
RetrocopyMASSFKKPQVASTSQKRKVGPKPELTEDQKQEVREAFDLFDADGSGTIDVKELKVAMRALGFEPRKEEMK
ParentalKMISEIDKEGTGKMNFSDFLTVMTQKMSEKDTKEEILKAFKLFDDDETGKISFKNLKRVAKELGENLTDE
.MISE.DKEGTGK..F.DFL.VMTQKM.EKDTKEEILKAF.LFDDDETGKISFKNLKRVA.ELGENLTDE
RetrocopyRMISEVDKEGTGKISFNDFLAVMTQKMAEKDTKEEILKAFRLFDDDETGKISFKNLKRVANELGENLTDE
ParentalELQEMIDEADRDGDGEVNEQEFLRIMKKTSLY
ELQEMIDEADRDGDGEVNE.EFLRIMKKT.LY
RetrocopyELQEMIDEADRDGDGEVNEEEFLRIMKKTNLY

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 7 .96 RPM
SRP014902_testis 0 .57 RPM 29 .99 RPM
SRP018288_heart 0 .00 RPM 33 .71 RPM
SRP018288_kidney 0 .00 RPM 44 .33 RPM
SRP018288_liver 0 .00 RPM 35 .50 RPM
SRP018288_lung 0 .00 RPM 54 .99 RPM
SRP018856_adipose 0 .00 RPM 50 .47 RPM
SRP035408_brain 0 .00 RPM 72 .73 RPM
SRP035408_liver 0 .00 RPM 77 .94 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_57 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_57 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_57 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 28 parental genes, and 44 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003641 retrocopy
retro_amel_56,
Bos taurus ENSBTAG000000078441 retrocopy
retro_btau_170,
Canis familiaris ENSCAFG000000191701 retrocopy
retro_cfam_199,
Choloepus hoffmanni ENSCHOG000000102441 retrocopy
retro_chof_39,
Callithrix jacchus ENSCJAG000000163383 retrocopies
retro_cjac_106, retro_cjac_185, retro_cjac_316,
Cavia porcellus ENSCPOG000000120812 retrocopies
retro_cpor_1250, retro_cpor_21,
Equus caballus ENSECAG000000007961 retrocopy
retro_ecab_49,
Felis catus ENSFCAG000000049011 retrocopy
retro_fcat_47,
Homo sapiens ENSG000001474001 retrocopy
retro_hsap_71,
Gorilla gorilla ENSGGOG000000113781 retrocopy
retro_ggor_74,
Loxodonta africana ENSLAFG000000144241 retrocopy
retro_lafr_121,
Microcebus murinus ENSMICG000000058622 retrocopies
retro_mmur_122, retro_mmur_21,
Myotis lucifugus ENSMLUG000000145202 retrocopies
retro_mluc_320, retro_mluc_370,
Macaca mulatta ENSMMUG000000207432 retrocopies
retro_mmul_1127, retro_mmul_176,
Mustela putorius furoENSMPUG000000118581 retrocopy
retro_mputfur_386,
Mus musculus ENSMUSG000000313472 retrocopies
retro_mmus_107, retro_mmus_838,
Nomascus leucogenys ENSNLEG000000138601 retrocopy
retro_nleu_1221,
Oryctolagus cuniculus ENSOCUG000000078971 retrocopy
retro_ocun_180,
Otolemur garnettii ENSOGAG000000053011 retrocopy
retro_ogar_236,
Procavia capensis ENSPCAG000000032031 retrocopy
retro_pcap_149,
Procavia capensis ENSPCAG000000077781 retrocopy
retro_pcap_364,
Pongo abelii ENSPPYG000000208331 retrocopy
retro_pabe_58,
Pan troglodytes ENSPTRG000000223891 retrocopy
retro_ptro_108,
Rattus norvegicus ENSRNOG000000170595 retrocopies
retro_rnor_2376, retro_rnor_2394, retro_rnor_2920, retro_rnor_304, retro_rnor_775,
Sus scrofa ENSSSCG00000012757 3 retrocopies
retro_sscr_1175, retro_sscr_57 , retro_sscr_822,
Ictidomys tridecemlineatus ENSSTOG000000238532 retrocopies
retro_itri_636, retro_itri_91,
Tarsius syrichta ENSTSYG000000038312 retrocopies
retro_tsyr_1142, retro_tsyr_36,
Tursiops truncatus ENSTTRG000000012362 retrocopies
retro_ttru_32, retro_ttru_335,


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