RetrogeneDB ID:

retro_sscr_6

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:9:38497414..38498620(+)
Located in intron of:ENSSSCG00000014994
Retrocopy
information
Ensembl ID:ENSSSCG00000014995
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DDI2
Ensembl ID:ENSSSCG00000003462
Aliases:None
Description:DNA-damage inducible 1 homolog 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:24578]


Retrocopy-Parental alignment summary:






>retro_sscr_6
ATGCTGCTCACTGTGTACTGTGTGCGGAAGGACCTCTCTGAGGCCACCTTCTCCCTCCAGGTCAGCCCTGACTTTGAGCT
GCACAACTTCCGTGTCCTCTGTGAGCTCGAGTCTGGCATTCCTGCCGAGGAAATTCAGATTGTCTACATGGAGCGACTCC
TTGGCGACGACCACTATTCCCTGGGCTCCTATGGCCTCAAAGACGGCGATGTCGTCGTCTTACTTCAGAAGGAGAATGTG
GGGTCCCGGGCTCCGGGACGGACATCCAGCCTGCCTCAGAGAGATTTCCCCGGGACAGCCGTGCCCGGGACGTCCAGCTC
CCGGCACCAGCATCAGCACCAGCACCAGCGCACACAGTCGGTCCAGCAGTCCCGCGGCATGGGCTCCGGAGAGAAGATGA
GCTCTGCCCAAGGACTGGACAGCCCCGCCCTGATCCGAAGCATGCTGCTCTCCAACCCCCATGACCTGTCCCTGCTGAAG
GAACGCAACCCCGCCTTGGCTGAAGCCCTGCTCAGTGGAAACCTAGAGACCTTTTCCCAGGTCCTGATGGAGCAGCAAAG
GGAAAGGGTCCTGAGGGAGCAAGAGAGATTTCGCCTCTACTCGGCTGACCCATTTGATTTGGAAGCTCAGGCCAAAATAG
AGGAAGAGATCCGGCAGCAGAACATTGAGGAAAACATGAATATCGCTATGGAAGAGGCCCCTGAGAGTTTCGGACAAGTG
GCCATGCTCTACATCAACTGCAAAGTGAACGGACATCCTTTGAAGGCTTTTGTTGACTCAGGTGCCCAGATGACCATTAT
GAGCCAAGCCTGTGCTGAGAGATGTAATATCATTCGGCTGGTGGACAGAAGATGGGCTGGGATTGCCAAAGGTGTGGGTA
CACAGAGAATTATTGGCCGAGTTCACCTAGCTCAGATTCAAATCGAAGGTGATTTCTTACAATGTTCTTTCTCTATACTC
GAGGAGCAGCCCATGGACATGCTTCTAGGGCTAGATATGCTCAGGAGACATCAATGTTCCATCGACCTGAAGAAAAACGT
GCTGGTGATCGGCACGACTGGCACACAGACTTACTTTCTTCCTGAGGGAGAGTTACCTCCGTGCGCTAAGTTGGTAAGTG
GAACTGGACAAGACGAGTCTTCAGACAAGGAAGTAGCAGATACTATTAAACATTCAGTCATGAATTCGGGACGAAAAAAG
CATTGA

ORF - retro_sscr_6 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.74 %
Parental protein coverage: 95.24 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMLLTVYCVRRDLSEVTFSLQVDADFELHNFRALCELESGIPAAESQIVYAERPLTDNHRSLASYGLKDGD
MLLTVYCVR.DLSE.TFSLQV..DFELHNFR.LCELESGIPA.E.QIVY.ER.L.D.H.SL.SYGLKDGD
RetrocopyMLLTVYCVRKDLSEATFSLQVSPDFELHNFRVLCELESGIPAEEIQIVYMERLLGDDHYSLGSYGLKDGD
ParentalVVILRQKENADPRPSVQFPNLPRIDFRSIAVPGTSNSR---QRQAQGVQQSHSSPG----EIASSPQGLD
VV.L.QKEN...R.......LP..DF...AVPGTS.SR...Q.Q.Q..Q....S.G....E..SS.QGLD
RetrocopyVVVLLQKENVGSRAPGRTSSLPQRDFPGTAVPGTSSSRHQHQHQHQRTQSVQQSRGMGSGEKMSSAQGLD
ParentalNPALLRDMLLANPHELSLLKERNPPLADALLSGDLEKFSRVLVEQQQDRARREQERIRLFSADPFDLEAQ
.PAL.R.MLL.NPH.LSLLKERNP.LA.ALLSG.LE.FS.VL.EQQ..R..REQER.RL.SADPFDLEAQ
RetrocopySPALIRSMLLSNPHDLSLLKERNPALAEALLSGNLETFSQVLMEQQRERVLREQERFRLYSADPFDLEAQ
ParentalAKIEEDIRQQNIEENMTIAMEEAPESFGQVVMLYINCKVNGHPVKAFVDSGAQMTIMSQACAERCNIMRL
AKIEE.IRQQNIEENM.IAMEEAPESFGQV.MLYINCKVNGHP.KAFVDSGAQMTIMSQACAERCNI.RL
RetrocopyAKIEEEIRQQNIEENMNIAMEEAPESFGQVAMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIIRL
ParentalVDRRWAGIAKGVGTQKIIGRVHLAQVQIEGDFLACSFSILEEQPMDMLLGLDMLKRHQCSIDLKKNVLVI
VDRRWAGIAKGVGTQ.IIGRVHLAQ.QIEGDFL.CSFSILEEQPMDMLLGLDML.RHQCSIDLKKNVLVI
RetrocopyVDRRWAGIAKGVGTQRIIGRVHLAQIQIEGDFLQCSFSILEEQPMDMLLGLDMLRRHQCSIDLKKNVLVI
ParentalGTTGSQTTFLPEGELPECARLAYGAGREEVRPEEIAD
GTTG.QT.FLPEGELP.CA.L..G.G..E....E.AD
RetrocopyGTTGTQTYFLPEGELPPCAKLVSGTGQDESSDKEVAD

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 6 .24 RPM
SRP014902_testis 0 .14 RPM 8 .35 RPM
SRP018288_heart 0 .00 RPM 5 .53 RPM
SRP018288_kidney 0 .00 RPM 20 .19 RPM
SRP018288_liver 0 .00 RPM 27 .18 RPM
SRP018288_lung 0 .00 RPM 14 .36 RPM
SRP018856_adipose 0 .02 RPM 14 .64 RPM
SRP035408_brain 0 .00 RPM 1 .27 RPM
SRP035408_liver 0 .00 RPM 5 .75 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_sscr_6 retrocopy
EST ID Start End Identity Match Mis-match Score
EW637069 38497730 38497890 99.4 159 1 158

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_6 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_6 has 11 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_96
Pan troglodytes retro_ptro_570
Gorilla gorilla retro_ggor_143
Pongo abelii retro_pabe_158
Macaca mulatta retro_mmul_231
Callithrix jacchus retro_cjac_196
Mus musculus retro_mmus_67
Oryctolagus cuniculus retro_ocun_249
Bos taurus retro_btau_15
Canis familiaris retro_cfam_193
Equus caballus retro_ecab_110
Parental genes homology:
Parental genes homology involve 24 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000118731 retrocopy
retro_amel_10,
Bos taurus ENSBTAG000000187182 retrocopies
retro_btau_15, retro_btau_650,
Canis familiaris ENSCAFG000000162201 retrocopy
retro_cfam_193,
Callithrix jacchus ENSCJAG000000086251 retrocopy
retro_cjac_196,
Cavia porcellus ENSCPOG000000208851 retrocopy
retro_cpor_88,
Equus caballus ENSECAG000000007621 retrocopy
retro_ecab_110,
Homo sapiens ENSG000001973121 retrocopy
retro_hsap_96,
Gorilla gorilla ENSGGOG000000135371 retrocopy
retro_ggor_143,
Macropus eugenii ENSMEUG000000061481 retrocopy
retro_meug_1364,
Myotis lucifugus ENSMLUG000000306691 retrocopy
retro_mluc_68,
Macaca mulatta ENSMMUG000000199121 retrocopy
retro_mmul_231,
Monodelphis domestica ENSMODG000000035151 retrocopy
retro_mdom_282,
Mustela putorius furoENSMPUG000000163321 retrocopy
retro_mputfur_1509,
Mus musculus ENSMUSG000000785151 retrocopy
retro_mmus_67,
Oryctolagus cuniculus ENSOCUG000000238911 retrocopy
retro_ocun_249,
Otolemur garnettii ENSOGAG000000277091 retrocopy
retro_ogar_4,
Ochotona princeps ENSOPRG000000184481 retrocopy
retro_opri_4,
Pongo abelii ENSPPYG000000018411 retrocopy
retro_pabe_158,
Pan troglodytes ENSPTRG000000240591 retrocopy
retro_ptro_570,
Pteropus vampyrus ENSPVAG000000050841 retrocopy
retro_pvam_420,
Rattus norvegicus ENSRNOG000000122741 retrocopy
retro_rnor_2606,
Sus scrofa ENSSSCG00000003462 1 retrocopy
retro_sscr_6 ,
Ictidomys tridecemlineatus ENSSTOG000000194471 retrocopy
retro_itri_93,
Tarsius syrichta ENSTSYG000000025221 retrocopy
retro_tsyr_1120,


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