RetrogeneDB ID: | retro_cpor_188 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_1:22734610..22735211(-) | ||
| Located in intron of: | ENSCPOG00000011122 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RNF13 | ||
| Ensembl ID: | ENSCPOG00000000517 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_188
TACAAGTTTGAAAATGCATCTCAGACATTTGATGCTCTCCCAGCAAAATTTGATTATAGACCTCCAGCTGAAGGCTTAAA
GAGTTTTTTGATGAATTAAAAACCAGAGAATGCTTGTGAACCCATATCGCCTCCACCAGTAAAAGACAATTCACCTGGCA
CTTTCATCATGTTCATTAGAAGACTTGATTGTAATTTTGATGGAAAGGTTTTAAGTGCACGGAGCGGGATACAAAGCAGC
CGATGTTCACAGTGTGGGTCTCAGGACCTCCATGGCCTGGGTCCAGCCATATCAATGTGTTACAAAAAATTGCCATCCCA
TCTGTGTCTGTGGGTGAGTCGTCAGCTGATTCCCTGGAAGATGAATTCACATGTGGAAAAGGGGGCCACAGTGTCTTAGT
TCCAGGGTGTAGTCTTCCTCTAGAATACTGTCTGGTCCCCTCTGCAGTATAGCACACATCTGTCTCATCCCAATAGCCAC
TTTTATGATCACAAAATTTGCCCAGGACACACATAGAGCCGGAAGGAATAGGCTTGGTAAAGATCAACATAAGAAACTCC
CTGTACGTAAATGTAAGAAAGGAGATGAGGATGATGTGTGT
ORF - retro_cpor_188 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.33 % |
| Parental protein coverage: | 58.89 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | YNFENASQTFDDLPAKFGYRPPAEGLKGFLINSKPENACEPIMPPPVKDNSSGTFIVLIRRLDCNFDIKV |
| Y.FENASQTFD.LPAKF.YRPPAEGLK.FL.N.KPENACEPI.PPPVKDNS.GTFI..IRRLDCNFD.KV | |
| Retrocopy | YKFENASQTFDALPAKFDYRPPAEGLKSFLMN*KPENACEPISPPPVKDNSPGTFIMFIRRLDCNFDGKV |
| Parental | LNAQRAG-YKAAIVHNV-DSEDLISM-GSNDIDVLKKIDIPSVFIGESSANSLKDEFTYEKGGHIILVPE |
| L.A.R.G.YKAA.VH.V..S.DL....GS..I.VL.KI.IPSV..GESSA.SL.DEFT..KGGH..LVP. | |
| Retrocopy | LSA-RSG>YKAADVHSV<GSQDLHGL<GSSHINVLQKIAIPSVSVGESSADSLEDEFTCGKGGHSVLVPG |
| Parental | FSLPLEYYLIPFLI-IVGICLILIVIFMITKFVQDRHRARRNRLGKDQLKKLPVHKFKKGDEYDVC |
| .SLPLEY.L.P....I..ICLI.I..FMITKF.QD.HRA.RNRLGKDQ.KKLPV.K.KKGDE.DVC | |
| Retrocopy | CSLPLEYCLVPSAV<IAHICLIPIATFMITKFAQDTHRAGRNRLGKDQHKKLPVRKCKKGDEDDVC |
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 | 28 .82 RPM |
| SRP017611_kidney | 0 .00 RPM | 29 .21 RPM |
| SRP017611_liver | 0 .00 RPM | 37 .30 RPM |
| SRP040447_lung | 0 .00 RPM | 41 .06 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 13 .27 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_188 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_188 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 | ENSCPOG00000000517 | 1 retrocopy |
retro_cpor_188 ,
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