RetrogeneDB ID: | retro_cpor_277 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_113:949590..950817(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SLC30A5 | ||
| Ensembl ID: | ENSCPOG00000003972 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_277
TCCTTTCCCATGTTTATTAGTGCTCTCCTTTTTAGAAATTTTTGGACATGCCCAATAACAGTCCAGCTTCAGGCTATGAA
CAGAGCTACACACCAGGAGGGCGTGGAGAACATCCTGTTTGGAGGAATGATCCTCAGTGCTGTGTTCTTCGCTTTGTCTG
TCAACATTTTATCATTTTGCTCTACAAAGGAGAGAGAGGTACCCTTATTGGGTTTTCTCCTGAAGGAACACCTCTTTATA
ACTTCATGGATGATGCTTTCAGCACAACTCTCAATCAACCACTAGGTTTAATAAGGAATCACCAAAACAAATTCTTGAAG
CGAGTGACTCTAGGCAGATCTTTTACTTCCTGTGCTTGAATCTGCTCTTTACCTTGGTGGAATTCTTCTATACTGTGTCG
ACCAATAGTCTGAGTCTGATCTCAGATAGATTTCAGATGCTCTTTGATTACCCTGCTTGGATCATGGGACTTTTTGCTGT
TCTGATGAATAGATGGAAAGCTACTCCAATTTTCTCCTATGGGTATGGTCAAGTAGAAATTCTCTCTGGATTGATTAATG
TACTTTTCTAATAATAATAGATTTTTGTGTTTATGGATCAGTTACTAGATTGATTGACCCTTCAGAATTAGGCAAGAACA
TGTTGACACCAGTCTAAGTTGGAGAACTGACCATAAACCTTATTGCTATTTGTGCCTTTAGCCATGTCCATAGCCACAAC
CATGGAACTTCACAAAGAAGCTGTCACTCATCTGATCACAGCCACTCACATCAAACACATGGACATAGTGACCATGGGCA
TGGTCAGAGCCACAGACCCCAAGGCAGAGGCATTAGTGCCAACAATGAGGGGTGTATTTCTGCATGTTTTCACAGACACA
CTTGGCAGTATTTGTATGATTGTTTCTACAGTTCTGACAGAGCAGTTTAGGTGGTTCTTTGCCAATTCCTCTGTTCACTT
TTTATTGTTGTGTTTTTAGTTCTCAGTGTTGTCTGTCCCACTGATTGAAGATGCCTGTCAAGTTCTGCATCTAAGGCTGC
TACAAGAACATGAGAAAATAAATAGACTGCTTGAGAAAATATACATAAAATGGAAGGATTAATATCATATCAATACCCTT
ATTTTTGGCATAATTCTACCAGTATTATAACAAGAACAATTCATATACAGGTAACACCTGATGTGCTAGAACAAAGAATA
GTACAGTAGATTACAGGAATACTGGAG
ORF - retro_cpor_277 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.57 % |
| Parental protein coverage: | 53.52 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | SFPIFISALLFGNFWTHPITDQLRAMNRATHQESTEHVLSGGVVVSAVFFILSANILSSPSKR-GQKGTL |
| SFP.FISALLF.NFWT.PIT.QL.AMNRATHQE..E..L.GG...SAVFF.LS.NILS..S...G..GTL | |
| Retrocopy | SFPMFISALLFRNFWTCPITVQLQAMNRATHQEGVENILFGGMILSAVFFALSVNILSFCSTK<GERGTL |
| Parental | IGYSPEGTPLYNFMGDAF-QHSSQSIPRFIKESLKQILEESDSRQIFYFLCLNLLFTFVELFYGVLTNSL |
| IG.SPEGTPLYNFM.DAF.QH.SQS..RF.KES.KQILE.SDSRQIFYFLCLNLLFT.VE.FY.V.TNSL | |
| Retrocopy | IGFSPEGTPLYNFMDDAF<QHNSQSTTRFNKESPKQILEASDSRQIFYFLCLNLLFTLVEFFYTVSTNSL |
| Parental | GLISDGFHMLFDCSALVMGLFAALMSRWKATRIFSYGYGRIEILSGFINGLF-LIVIAFFVFMESVARLI |
| .LISD.F.MLFD..A..MGLFA.LM.RWKAT.IFSYGYG..EILSG.IN.LF.LI.I.F.V...SV.RLI | |
| Retrocopy | SLISDRFQMLFDYPAWIMGLFAVLMNRWKATPIFSYGYGQVEILSGLINVLF<LIIIDFCVY-GSVTRLI |
| Parental | DPPELDTNMLTPVSVGGLIVNLIGICAFSHAHSHSHGTSQGGCHSSDHSHSHHTHGHSDHGHSHSHGPSG |
| DP.EL..NMLTPV.VG.L..NLI.ICAFSH.HSH.HGTSQ..CHSSDHSHSH.THGHSDHGH..SH.P.G | |
| Retrocopy | DPSELGKNMLTPV*VGELTINLIAICAFSHVHSHNHGTSQRSCHSSDHSHSHQTHGHSDHGHGQSHRPQG |
| Parental | GGMNAN-MRGVFLHVLADTLGSIGVIVSTVLIEQFGWFVADP-LCSLF-IAVLIFLSV-VPLIKDACQVL |
| .G..AN.MRGVFLHV..DTLGSI..IVSTVL.EQF.WF.A...LCSLF....L....V.VPLI.DACQVL | |
| Retrocopy | RGISAN>MRGVFLHVFTDTLGSICMIVSTVLTEQFRWFFANS<LCSLFIVVFLVLSVV>VPLIEDACQVL |
| Parental | LLRLPPEHE-KELHTALEKIQKIEGLISYRDPHFWRHSASIVAGTIHIQVTSDVLEQRIVQQVTGILK |
| .LRL..EHE.....TA.E.I.K.EGLISY..P.FW..S.SI...TIHIQVT.DVLEQRIVQ..TGIL. | |
| Retrocopy | HLRLLQEHE<ENK*TA*ENIHKMEGLISYQYPYFWHNSTSIITRTIHIQVTPDVLEQRIVQ*ITGILE |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 32 .50 RPM |
| SRP017611_kidney | 0 .00 RPM | 57 .37 RPM |
| SRP017611_liver | 0 .00 RPM | 46 .44 RPM |
| SRP040447_lung | 0 .00 RPM | 55 .33 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 17 .74 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_277 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_277 was not experimentally validated.
Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000003972 | 1 retrocopy |
retro_cpor_277 ,
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