RetrogeneDB ID: | retro_cpor_447 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_16:11128764..11129875(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DTL | ||
| Ensembl ID: | ENSCPOG00000014965 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_447
AGGCTTTGTAGCATAGAATCACAAACTAGTAGAAAAAAGTGCTTCAAAGAATGGATGGCTCACTGGAATGCTATCTTTGA
CTTGGCCTGGGTCCCAGGCAAGCTCAAACTTGTTACAGCAGCCAGTGATCAAACAGCCAAATTTTGGGACATAAAAGCTG
GTGAGTTGATTGGAACATGCAAGGTCATCAGTGCAGTCTCAAGTCAGTTGCGCTTTCTAAGTTTTAGAAAGTGTATCCTG
TACAGGTGGAAGAGACAGTAACATGATGGTCTGGGATACCAGTTGCAGTAAAAAAGATGGGTTCTAGGGGCAAGTGAACT
AAATCAATGGAACTTATAATCTGTCAGACAAGCAAACACCTTCAAAGTCCAAAAAGAAACAGAATTCTAAAGAACTTGTT
CCTTCTGTGAATTTCCAGAAGAGTGTTACTATAGCTGTTTTTCCAAGATGAGAATACAATAGTTTCAGGAGGAGCTGTGG
ATGGAATAATAAAAATATGGGATTTACACAAGAATTTTACTGCTTATTGACAAGAATCTTTAACATCTAAATCTTTCTTG
TGCCCAGGTAGCAGCACTCAAAAACTAGGATACTCCAGTTGATTTTGTATTCAACTGGCACCACTTTATTTGCTAATTGC
ACAGAGGACAACATCTATATGTTCAGTATTACTGGATTAAAGACCTCTCTGGTTGTTGTCTTCAGTGGACACCAGAACTC
TATCTTTTACTAAAATCAAGTCTTAGTCCAGATGACCAGTTTTTACTCAGTGGTTTGAGTAATGAAGCTGCCCACATATG
GAAGGTCTCTACACCCTCGCATCCACCTACCGTGCTCCTGGGTCACTCTTAAGAGGTCAGTTTTGTGTGCTAGTGTTCGT
CTGACTTCACCAAAATTGCTACCTGCTCTGCTGACAGCACATTAAAAATCTGGCACTTGAATAGAGGCTTAGAGGAGAAA
CCAGGAGCAGATATGAATTCCATAGTGGGTCTGTTCCTCTCAGAAGAAAAAAACAGACAAGATCAAGCCTGTAGGAGTAA
AAAGTACCCAGAAGACACCTGTCAAAGCCCCAAGGGCAAAGAGCAACCCAAGCCTGAGTACAGAGCTGAGC
ORF - retro_cpor_447 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.86 % |
| Parental protein coverage: | 50.54 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | RLYNTETQTIRKKCFKEWMAHWNAVFDLAWVPGELKLVTAAGDQTAKFWDVKAGELIGTCK-GHQCSLKS |
| RL...E.QT.RKKCFKEWMAHWNA.FDLAWVPG.LKLVTAA.DQTAKFWD.KAGELIGTCK.GHQCSLKS | |
| Retrocopy | RLCSIESQTSRKKCFKEWMAHWNAIFDLAWVPGKLKLVTAASDQTAKFWDIKAGELIGTCK<GHQCSLKS |
| Parental | VAFSKFQK-AVFCTGGRDGNIMVWDTRCNKKDGFYRQVNQISGAHNTSDKQTPSKPKKKQNSKGLAPSVD |
| VA.SKF.K..V.CTGGRD.N.MVWDT.C.KKDGF..QVN.I.G..N.SDKQTPSK.KKKQNSK.L.PSV. | |
| Retrocopy | VALSKF*K<SVSCTGGRDSNMMVWDTSCSKKDGF*GQVN*INGTYNLSDKQTPSKSKKKQNSKELVPSVN |
| Parental | FQQSVTVVLF-QDENTLVSAGAVDGIIKIWDLRKNYTAYRQEPIASKFFLYPGSSTRKLGYSS-LILDST |
| FQ.SVT...F.QDENT.VS.GAVDGIIKIWDL.KN.TAY.QE...SK.FL.PGSST.KLGYSS.LIL.ST | |
| Retrocopy | FQKSVTIAVF>QDENTIVSGGAVDGIIKIWDLHKNFTAY*QESLTSKSFLCPGSSTQKLGYSS<LILYST |
| Parental | GSTLFANCTDDNIYMFNMTGLKTSPVAVFNGHQNSTFY-VKSSLSPDDQFLLSGSSDEAAYIWKVSTPWH |
| G.TLFANCT.DNIYMF..TGLKTS.V.VF.GHQNS.FY..KSSLSPDDQFLLSG.S.EAA.IWKVSTP.H | |
| Retrocopy | GTTLFANCTEDNIYMFSITGLKTSLVVVFSGHQNSIFY<LKSSLSPDDQFLLSGLSNEAAHIWKVSTPSH |
| Parental | PPTVLLGHSQEVTSVCWCPSDFTKIATCSDDNTLKIWRLNRGLEEKPGADKHSIVG-WASQKKKEARSGL |
| PPTVLLGHS.EV..VC.C.SDFTKIATCS.D.TLKIW.LNRGLEEKPGAD..SIVG...SQKKK...... | |
| Retrocopy | PPTVLLGHS*EVSFVC*CSSDFTKIATCSADSTLKIWHLNRGLEEKPGADMNSIVG>CSSQKKKTDKIKP |
| Parental | VAVPSTQSTPAKAPRVKSSPVLSSPSS |
| V.V.STQ.TP.KAPR.KS.P.LS...S | |
| Retrocopy | VGVKSTQKTPVKAPRAKSNPSLSTELS |
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 | 0 .46 RPM |
| SRP017611_kidney | 0 .00 RPM | 1 .47 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .52 RPM |
| SRP040447_lung | 0 .00 RPM | 5 .20 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 1 .61 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_447 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_447 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 | ENSCPOG00000014965 | 1 retrocopy |
retro_cpor_447 ,
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