RetrogeneDB ID: | retro_cpor_454 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_16:28754763..28756070(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MSR1 | ||
| Ensembl ID: | ENSCPOG00000022785 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_454
GTAAGAGAAGGCAGTATGGAGCAGCAGAATGTCTTTCTTGATCACCAGGAGGAGCCTGATAGCTCTTCAGATTCTGTGTA
ATTTGATGCTTGTTTAATAACAGCACTGCTTCCTCCCAATCCTAAAAATGGCCACCGAGAGAAACTGAAGTCCTTCAAAG
CTGCACTCATTGCCCTGTATCTCCTTGCACTTGTCACCCTGATACCTGTCATCAGCATAGTGGCAGCTCATCTTCTGAAG
TGGGAAGTGAAGAATTGCATGGTTGGTTCAGCTCATGCAAATGCTATGTCTCAAAGTCTTGGAAAATGAATGACAGTGAA
GATGCAATGAGATTTCCAGAAATTGTTTTGGGACACATCAACAACACTGAGAAAAAATACAGTACATTTCAGATGCAGAA
GCCAATTTCATAGGTTCAGAACACTTCCAAAATTTCAGTGTGACAACTGATCAAAGATTCAGTTATGCTTTTCTGCAGCT
AAGTACCTTAGTATCCTCAATCCAAGAACATAAGAACACAATACATGAGATCTCCAAACCCTTAGTAAGTCTGAATAGCA
CATTCCTTGATCTGCAGCTCAATATAGGAACATTGAATTTTTTAAAAGTCCAGGAGACTAAATTGAAGCAACACGAGGAT
ATTAGTAAATTGAAGGAGCATTATACAATGCATCAACAGAAATTAAGTCGCTAAAAGAGCAAGAGCATGTGGAAGGGGAA
TAAAGAAAGAGTTGAAAGTGCTGAAGAATATCACCAGTGATCTTAGCTTGAAAGATTGCAACCATTCTCTGAAATTGAAA
AATACAACTTTAATTCAAGGTTTCCCTGGACCCAGAGGTGAAAAAGGAGACAGAGATCCCACTGAAGAAATTGATATACC
AGGCATTCCAGGTCTAAGAGATCGTCCAGGTCTTAAAGGTGATACAGAAGGAGCTGGCTTTCCTGGAAGTAGAGGCTACT
TGGGACCAACAGGAAATGTGGGAAGGCCAGGAAATCCTGGACAAAAAGGTCAAAAAGGAGCAAAAGGAAGAAGGAGCATA
TTCCCTCTGCCAAGACAGTTCGACTGGCTAATGGTAAAGGCCACAGAAGGGTAGAAGGACATTTTCCAGGAGGGCCGTTA
GAGCACCATTTGGGATGATCGCTGGGAAATACAAGTTGCATCTGTCATCTGGTGAAGTTTGGAATACAAAGGTGTTCAAG
CTGTGCACAAAGTAGCTTATTTTGGACAAGGTACTGGTCCAATATGGTTGACTGAAGTATTTTGTTTTGGGAGAAAATTA
TCTATGGAGAAATGTAATATCAGGCAA
ORF - retro_cpor_454 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.4 % |
| Parental protein coverage: | 96.04 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | VFDSIMESRNIFLDHQEELDIYSDSVKFDARSMTALLPPNPKNGLQEKLKSFKAALIALYLLVFVVLIPV |
| V....ME..N.FLDHQEE.D..SDSV.FDA...TALLPPNPKNG..EKLKSFKAALIALYLL..V.LIPV | |
| Retrocopy | VREGSMEQQNVFLDHQEEPDSSSDSV*FDACLITALLPPNPKNGHREKLKSFKAALIALYLLALVTLIPV |
| Parental | ISIVAAHLLKREMKNCTVGSPHASAMSQSLGK-GNGSEDAMKFQEFVLEHISNIERR-IQDISDAEASFI |
| ISIVAAHLLK.E.KNC.VGS.HA.AMSQSLGK..N.SEDAM.F.E.VL.HI.N.E...IQ.ISDAEA.FI | |
| Retrocopy | ISIVAAHLLKWEVKNCMVGSAHANAMSQSLGK<MNDSEDAMRFPEIVLGHINNTEKK<IQYISDAEANFI |
| Parental | GSENFQNFSMTTDQRLNSVFLQLNNLVSSVQEHESAVDEISKSLVSLNTTLLDLQLSIETLN-KKVQETT |
| GSE.FQNFS.TTDQR....FLQL..LVSS.QEH.....EISK.LVSLN.T.LDLQL.I.TLN..KVQET. | |
| Retrocopy | GSEHFQNFSVTTDQRFSYAFLQLSTLVSSIQEHKNTIHEISKPLVSLNSTFLDLQLNIGTLNFLKVQETK |
| Parental | LKQQEDISKLKEH-VYNASAEIKSLKEEQEHIEEE-IKKELKVLNNVTNDLRLKDWEHSLTLRNITLIQG |
| LKQ.EDISKLKEH..YNAS.EIKSLKE.QEH.E.E.IKKELKVL.N.T.DL.LKD..HSL.L.N.TLIQG | |
| Retrocopy | LKQHEDISKLKEH<LYNASTEIKSLKE-QEHVEGE<IKKELKVLKNITSDLSLKDCNHSLKLKNTTLIQG |
| Parental | PPGPRGEKGDRGAPGQTGIPGLPGLRGPPGLKGDRGVTGFPGSKGYPGPAGNVGRPGNPGQKGQKGEKGT |
| .PGPRGEKGDR.......IPG.PGLR..PGLKGD....GFPGS.GY.GP.GNVGRPGNPGQKGQKG.KG. | |
| Retrocopy | FPGPRGEKGDRDPTEEIDIPGIPGLRDRPGLKGDTEGAGFPGSRGYLGPTGNVGRPGNPGQKGQKGAKGR |
| Parental | GNLFHLP-NVVRLVNGK-VPHEGR-VEIFHEGIWGTICDDRWEIRVATVICRSLGYKGAKAVHKAAYFGQ |
| ...F.LP...VRL.NGK..P..GR...IF.EG...TI.DDRWEI.VA.VI..SL.YKG..AVHK.AYFGQ | |
| Retrocopy | RSIFPLP<KTVRLANGK<RPQKGR<KDIFQEGR*STIWDDRWEIQVASVIW*SLEYKGVQAVHKVAYFGQ |
| Parental | GTGPIWLNE-FCFGRESSIDQCNIRQ |
| GTGPIWL.E.FCFGR..S...CNIRQ | |
| Retrocopy | GTGPIWLTEVFCFGRKLSMEKCNIRQ |
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 .06 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .42 RPM |
| SRP017611_liver | 0 .00 RPM | 21 .85 RPM |
| SRP040447_lung | 0 .00 RPM | 63 .46 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 0 .21 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_454 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_454 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 | ENSCPOG00000022785 | 1 retrocopy |
retro_cpor_454 ,
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