RetrogeneDB ID: | retro_cpor_504 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_17:37759503..37759853(-) | ||
| Located in intron of: | ENSCPOG00000005816 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MREG | ||
| Ensembl ID: | ENSCPOG00000010037 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_504
CTGCAGCAGATTCGAAGGGAAGTGAGAAACAGATGGAAACGCATTTTAGAAGATTTAGGTTTTCAAAAGGAAGTGGATTC
TTTGTTGTCAGTGACTAAACTTAGCACCATGAGTGAGTCTAAAAATACGAGGAAAGCCCAAGAGATGTTGTTGAAAGTGG
CTAAGAGACCAGCATTTTTCCAACCAGTTGGGAGCTGTCAGGGAGACACCTATGTGTTGTGGATCGACCCATTCATTGCT
CTTGAGCAGCTGAAGAGTTCTCTAAGATTGCTAGTCAACCTTCGCCCAAGAAGCCTGGGCGATGCCTAGCTGATGACCAG
AGAAAACAACCCTGCCTTCCATTTCCAAGT
ORF - retro_cpor_504 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.51 % |
| Parental protein coverage: | 54.67 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LRQIRREVRNRWKRILEDLGFQKEVDSLLSVTKLSTMSDSKNTRKAREMLLKLAE-ETSIFPTSWELSER |
| L.QIRREVRNRWKRILEDLGFQKEVDSLLSVTKLSTMS.SKNTRKA.EMLLK.A..ETSIFPTSWELS.R | |
| Retrocopy | LQQIRREVRNRWKRILEDLGFQKEVDSLLSVTKLSTMSESKNTRKAQEMLLKVAK<ETSIFPTSWELSGR |
| Parental | YLFVVDRLIALD-AAEEFFKIASQTYPKKPGVPCLANDQKKQPYLPFPS |
| .L.VVDR.I....AAEEF.KIASQ..PKKPG..CLA.DQ.KQP.LPFPS | |
| Retrocopy | HLCVVDRPIHCS*AAEEFSKIASQPSPKKPG-RCLADDQRKQPCLPFPS |
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 | 5 .06 RPM |
| SRP017611_kidney | 0 .00 RPM | 6 .60 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .61 RPM |
| SRP040447_lung | 0 .00 RPM | 18 .89 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 2 .52 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_504 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_504 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000010037 | 1 retrocopy |
retro_cpor_504 ,
|
| Mustela putorius furo | ENSMPUG00000007637 | 1 retrocopy |