RetrogeneDB ID:

retro_sscr_51

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:1:224957411..224959265(-)
Located in intron of:ENSSSCG00000028884
Retrocopy
information
Ensembl ID:ENSSSCG00000005150
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSSCG00000012637
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sscr_51
ATGAAAGTGTCTCTTGGTAACGGTGAAATGGGCGTCTCTGCCCATTTACAGCCTTGCAAGGCAGGAACCACACGGTTTTT
TACCAGCAATACTCACAGTTCGGTGGTATTGCAAGGCTTTGATCAGCTTAGAATAGAAGGATTGCTTTGTGATGTGACTC
TGGTACCAGGTGATGGAGATGAAATCTTCCCTGTTCATCGAGCTATGATGGCGTCTGCTAGTGATTATTTCAAGGCTATG
TTCACAGGTGGAATGAAAGAACAAGATTTAATGTGCATTAAGCTTCACGGTGTGAACAAAGTTGGTCTGAAGAAAATAAT
TGATTTTATTTATACTGCAAAACTTTCTCTTAATATGGACAATCTTCAGGACACACTTGAAGCTGCCAGCTTTTTGCAAA
TTCTACCTGTTTTGGACTTCTGTAAAGTGTTTCTTATTTCAGGAGTCTCTTTAGATAACTGTGTTGAGGTTGGACGAATT
GCTAACACCTACAATCTTATAGAAGTAGATAAATATGTCAATAATTTCATCCTGAAGAATTTTCCTGCATTATTGAGTAC
TGGGGAGTTTCTAAAACTCCCTTTTGAACGGCTTGCCTTTGTGCTTTCCAGCAACAGTCTTAAGCACTGTACTGAACTTG
AGCTTTTCAAGGCTGCGTGTCGCTGGCTAAGGTTGGAAGACCCTCGGATGGATTATGCTGCAAAATTAATGAAGAACATT
CGATTTCCACTGATGACACCACAGGATCTCATCAATTATGTGCAGACAGTAGATTTCATGAGAACAGACAATACTTGTGT
GAATTTGCTTTTGGAAGCTAGCAATTACCAAATGATGCCATATATGCAGCCAGTGATGCAGTCAGATAGAACTGCCATTA
GATCTGACTCTACCCACTTGGTTACATTAGGAGGAGTTTTGAGGCAGCAGCTGGTTGTCAGTAAAGAATTACGGATGTAT
GATGAAAGAGCTCAAGAGTGGAGGTCTTTAGCCCCCATGGATGCTCCTCGTTACCAGCATGGCATTGCTGTCATTGGAAA
CTTTCTTTATGTTGTTGGTGGTCAAAGTAATTATGATACAAAAGGAAAAACTGCTGTTGATACAGTTTTCAGATTTGATC
CCCGGTATAATAAATGGATGCAGGTTGCATCATTAAATGAAAAGCGCACATTTTTCCACTTAAGTGCTCTGAAAGGGCAT
TTGTATGCTGTTGGTGGGCGAAGTGCAGCTGGTGAACTGGCCACAGTAGAATGTTACAATCCAAGAATGAATGAGTGGAG
CTATGTTGCAAAAATGAATGAACCCCACTATGGCCATGCTGGAACAGTATATGGAGGCTTAATGTATATTTCAGGAGGAA
TTACTCATGACACTTTCCAAAACGAGCTCATGTGTTTTGACCCTGATACGGACAAATGGACACAGAAGGCTCCAATGACT
ACAGTCAGAGGTCTGCACTGCATGTGTACAGTTGGAGATAAGCTCTATGTCATTGGTGGCAATCACTTCAGAGGAACAAG
TGATTATGATGATGTTCTAAGCTGTGAATACTATTCACCAACCCTTGACCAGTGGACACCAATTGCTGCCATGTTAAGAG
GCCAGAGTGATGTTGGAGTTGCCGTCTTTGAAAATAAAATCTATGTTGTAGGTGGATATTCTTGGAATAATCGTTGTATG
GTGGAAATTGTCCAAAAATACGACCCAGAAAAGGATGAGTGGCATAAAGTTTTTGATCTTCCAGAATCACTTGGTGGCAT
TCGAGCTTGTACTCTCACAGTTTTTCCACCTGAAGAAAACCCTGGATCACCTTCTAGAGAATCACCTCTATCAGCACCTT
CAGATCATTCTTAG

ORF - retro_sscr_51 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.47 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalLKTGLSIASLLFMASVFVFCFLFLFLFLVTLDNCVEVGRIANTYNLTEVDKYVNSFVLKNFPALLSTGEF
L...L..AS.L....V..FC..FL....V.LDNCVEVGRIANTYNL.EVDKYVN.F.LKNFPALLSTGEF
RetrocopyLQDTLEAASFLQILPVLDFCKVFL-ISGVSLDNCVEVGRIANTYNLIEVDKYVNNFILKNFPALLSTGEF
ParentalLKLPFERLAFVLSSNSLKHCTELELFKATCRWLRLEEPRMDFAAKLMKNIRFPLMTPQELINYVQTVDFM
LKLPFERLAFVLSSNSLKHCTELELFKA.CRWLRLE.PRMD.AAKLMKNIRFPLMTPQ.LINYVQTVDFM
RetrocopyLKLPFERLAFVLSSNSLKHCTELELFKAACRWLRLEDPRMDYAAKLMKNIRFPLMTPQDLINYVQTVDFM
ParentalRTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDTTHLVTLGGVLRQQLVVSKELRMYDEKAHEWKSL
RTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSD.THLVTLGGVLRQQLVVSKELRMYDE.A.EW.SL
RetrocopyRTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDSTHLVTLGGVLRQQLVVSKELRMYDERAQEWRSL
ParentalAPMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKGY
APMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKG.
RetrocopyAPMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKGH
ParentalLYAVGGRNAAGELPTVECYNPRTNEWTYVAKMSEPHYGHAGTVYGGVMYISGGITHD-FQKELMCFDPDT
LYAVGGR.AAGEL.TVECYNPR.NEW.YVAKM.EPHYGHAGTVYGG.MYISGGITHD.FQ.ELMCFDPDT
RetrocopyLYAVGGRSAAGELATVECYNPRMNEWSYVAKMNEPHYGHAGTVYGGLMYISGGITHDTFQNELMCFDPDT
ParentalDKWIQKAPMTTVRGLHCMCTVGERLYVIGGNHFRGTSDYDDVLSCEYYSPILDQWTPIAAMLRGQSDVGV
DKW.QKAPMTTVRGLHCMCTVG..LYVIGGNHFRGTSDYDDVLSCEYYSP.LDQWTPIAAMLRGQSDVGV
RetrocopyDKWTQKAPMTTVRGLHCMCTVGDKLYVIGGNHFRGTSDYDDVLSCEYYSPTLDQWTPIAAMLRGQSDVGV
ParentalAVFENKIYVVGGYSWNNRCMVEIVQKYDPDKDEWHKVFDLPESLGGIRACTLTVFPPEETTPSPSRESPL
AVFENKIYVVGGYSWNNRCMVEIVQKYDP.KDEWHKVFDLPESLGGIRACTLTVFPPEE...SPSRESPL
RetrocopyAVFENKIYVVGGYSWNNRCMVEIVQKYDPEKDEWHKVFDLPESLGGIRACTLTVFPPEENPGSPSRESPL
ParentalSAP
SAP
RetrocopySAP

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 10 .62 RPM 0 .00 RPM
SRP014902_testis 19 .66 RPM 7 .64 RPM
SRP018288_heart 18 .94 RPM 1 .13 RPM
SRP018288_kidney 30 .93 RPM 24 .63 RPM
SRP018288_liver 22 .23 RPM 0 .96 RPM
SRP018288_lung 22 .10 RPM 9 .98 RPM
SRP018856_adipose 24 .42 RPM 22 .26 RPM
SRP035408_brain 10 .29 RPM 36 .33 RPM
SRP035408_liver 16 .23 RPM 1 .70 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_51 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_51 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_51 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000017821 retrocopy
retro_amel_749,
Bos taurus ENSBTAG000000005011 retrocopy
retro_btau_44,
Canis familiaris ENSCAFG000000182721 retrocopy
retro_cfam_422,
Callithrix jacchus ENSCJAG000000024471 retrocopy
retro_cjac_3406,
Cavia porcellus ENSCPOG000000112681 retrocopy
retro_cpor_590,
Equus caballus ENSECAG000000082371 retrocopy
retro_ecab_622,
Loxodonta africana ENSLAFG000000081221 retrocopy
retro_lafr_1018,
Myotis lucifugus ENSMLUG000000273931 retrocopy
retro_mluc_204,
Macaca mulatta ENSMMUG000000022931 retrocopy
retro_mmul_42,
Mustela putorius furoENSMPUG000000017301 retrocopy
retro_mputfur_169,
Mus musculus ENSMUSG000000367821 retrocopy
retro_mmus_121,
Nomascus leucogenys ENSNLEG000000147361 retrocopy
retro_nleu_1031,
Oryctolagus cuniculus ENSOCUG000000019931 retrocopy
retro_ocun_254,
Pongo abelii ENSPPYG000000206581 retrocopy
retro_pabe_60,
Pteropus vampyrus ENSPVAG000000159891 retrocopy
retro_pvam_1485,
Rattus norvegicus ENSRNOG000000140291 retrocopy
retro_rnor_154,
Sus scrofa ENSSSCG00000012637 1 retrocopy
retro_sscr_51 ,
Ictidomys tridecemlineatus ENSSTOG000000120351 retrocopy
retro_itri_124,
Tarsius syrichta ENSTSYG000000025211 retrocopy
retro_tsyr_19,
Tursiops truncatus ENSTTRG000000140981 retrocopy
retro_ttru_26,
Vicugna pacos ENSVPAG000000030911 retrocopy
retro_vpac_8,


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