RetrogeneDB ID: | retro_cpor_817 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_29:26499591..26500715(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCPOG00000020847 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TINF2 | ||
| Ensembl ID: | ENSCPOG00000014800 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_817
CTTGGCCGCCCCAAGGGGGCCGGTCCAGCCACTGGGCGCTTTGTGGCCGCAGCCAGCTTGCAAGTGGTGCGCGAATGCTG
CGGGGAGCATTTCCCTGAGTCCTCCAGCTTCTGAGCTCCCTCTAGGCTGCCGCCCCGGCTTGGTTCGCTACCGGCACCAT
GAGCGCTTGTATATGGGCCTACAGGCCAAGATGGTGGTGGAGATGATCTAGGAGGGCGGCCTTGGCCTCAGGTTCTAAGT
GTCCTGAAATTCCCACAGTCTGGACTTGTACCGCGGGACCCTAAAGCTACAGAGTGGGATCTGAAGATTTTGGAGGCACG
GGAGACCTTTTGCCAGCAGGTGAAGCAACTGTCAGAGGCCCCCGTGAATTTGGCCTCAAAGCTACAGGAGCTTGAAGAAG
AATATGGGGAACCCTTTATGACCGCCATGGAGAAGCTGTTTTTTGAATATTTGTGTCAGCTAGAGAGAGCATTGCCTACC
ATACAGGTACAGCAGCTTCAAGATGTGCTGAGTTGGATGCAGCCTGAAGTTCCTGTCCCCTCTTCTCCTGCCTTGAGCCA
GTATGCTGTGGACATGGGGTGGCCACTTCCAGAGCACTTTGTTTCTAATTCAGTGAACTTGACTGAGCCTGTGGGACAGA
ATCCTCCTACGCAGTCTAGACCAGCTCTCCACAGTCCTCTGCCAAAAGCCAAGCTGAGCCCTGGGGGACCAGCTTCAAAG
AAGCATCAAGAATCTTTTGCTGGCCATCACTTCAATCTGGCCCCACTAGGTCGGCGAAGACGCCAGTCCCGATGGACATC
TGCGAGGGGCGGCTACAAAGAATGCCCCACACTCATGCTGTTGCCCTTTAGGAATCTGGACCCACCAACCCAAGTCATAG
CTCAACCTGAGGGCAGGGAAGAGCATGGGATGCACACAGCAGACACAGCAGGTGTGGGCACAAAAGCAGCCATCACCAGC
AAGTCAAAGAGTCCATATCAAATTCTGGGGGAAAGGCTCTGAAGGAAAACCCACCTGCCTTGTCTGCCTCAGGGGAAATT
GAGAATTGCTTGGATTGTTACTTGGAACCCCTGAGACTACCCTTATCACCTCCAGAGGCCAAGAAGCCAGCACGTTGTCC
ATCT
ORF - retro_cpor_817 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.51 % |
| Parental protein coverage: | 84.41 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAPKGAGPATWRIAAAASWQVVRERYVEHFPR-VLQFLRSLRAAAP-GLVRYRHHERLCMGLQAKMVVE |
| ...PKGAGPAT.R..AAAS.QVVRE...EHFP..VLQ.L.SL.AAAP.GLVRYRHHERL.MGLQAKMVVE | |
| Retrocopy | LGRPKGAGPATGRFVAAASLQVVRECCGEHFPE<VLQLLSSL*AAAP<GLVRYRHHERLYMGLQAKMVVE |
| Parental | MI-VRGRPWPQVLSVLNRHFPESGLIPRDPKAKEQDLKILEARETFCQQVKQLSEAPVNLASTLQQELEE |
| MI...GRPWPQVLSVL...FP.SGL.PRDPKA.E.DLKILEARETFCQQVKQLSEAPVNLAS.LQ.ELEE | |
| Retrocopy | MI<LGGRPWPQVLSVLK--FPQSGLVPRDPKATEWDLKILEARETFCQQVKQLSEAPVNLASKLQ-ELEE |
| Parental | EYGEAFMTAMEKLFFEYLCQLERALPTIQAQQLQDVLSWMQPEVPVPSSLALSQYAVDMGWPLPEHFVSN |
| EYGE.FMTAMEKLFFEYLCQLERALPTIQ.QQLQDVLSWMQPEVPVPSS.ALSQYAVDMGWPLPEHFVSN | |
| Retrocopy | EYGEPFMTAMEKLFFEYLCQLERALPTIQVQQLQDVLSWMQPEVPVPSSPALSQYAVDMGWPLPEHFVSN |
| Parental | SVNLTEPVGQNPPTQSRPALHSPLPKAKLSPGGPASKKHRESFAGHHFNLAPLGRRRCQSRWTSARGSYK |
| SVNLTEPVGQNPPTQSRPALHSPLPKAKLSPGGPASKKH.ESFAGHHFNLAPLGRRR.QSRWTSARG.YK | |
| Retrocopy | SVNLTEPVGQNPPTQSRPALHSPLPKAKLSPGGPASKKHQESFAGHHFNLAPLGRRRRQSRWTSARGGYK |
| Parental | ERPTVMLLPFRNLDPPSQVIAQPEGREEHGMHTADTAGVGTKAAITSKSKSPSQIL-GGKALKENPPALS |
| E.PT.MLLPFRNLDPP.QVIAQPEGREEHGMHTADTAGVGTKAAITSKSKSP.QIL.GGKALKENPPALS | |
| Retrocopy | ECPTLMLLPFRNLDPPTQVIAQPEGREEHGMHTADTAGVGTKAAITSKSKSPYQIL<GGKALKENPPALS |
| Parental | ASGEMENCLGCYLEPLRLPLSPSEAKKPAHCPS |
| ASGE.ENCL.CYLEPLRLPLSP.EAKKPA.CPS | |
| Retrocopy | ASGEIENCLDCYLEPLRLPLSPPEAKKPARCPS |
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 .12 RPM | 15 .30 RPM |
| SRP017611_kidney | 0 .00 RPM | 16 .12 RPM |
| SRP017611_liver | 0 .04 RPM | 9 .58 RPM |
| SRP040447_lung | 0 .00 RPM | 16 .54 RPM |
| SRP040447_skeletal_muscle | 0 .01 RPM | 4 .54 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_817 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_817 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 | ENSCPOG00000014800 | 1 retrocopy |
retro_cpor_817 ,
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