RetrogeneDB ID: | retro_cpor_399 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_14:24647631..24648049(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GLOD5 | ||
| Ensembl ID: | ENSCPOG00000003997 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_399
ACTCCAAGGATTCAGTCATGGAGTTACAGCAGTCCTTCCTCGTGTTTTATTCATAGACTCAACCACATGTAAAGACAGAA
AAGAACATCAAAGACTTCTGCATGTTTTACTCCAAAATCATGCATACCGAGACCCTAGCTTTCAAGAGAAACTGTAAAGT
GCTGTGTCTTAGAGACCAGATTTTTGACCTCCGTTAGAGGGGGAAGAAATTGAACCTAAAGCCATTCACCCACTCTGCAG
CTACACAGATATATGTTTGATCACAGAGATGCCTTTGGAGATCATTTAGCACCTTCAAGCTTTTGGTGACCTCAATGAAA
ATTGCTCATTCCTCAGAACAGGAGCAAAAGGGCCTATTATGTCCATCTGCTTCTGAGTCACATACAGAAATCTGATTGTG
TTGTCCAATTACCTCTCC
ORF - retro_cpor_399 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.06 % |
| Parental protein coverage: | 97.32 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | TAGTQSWRNSSQTLSPSPCLIQRLDHI-VMTVKSIKDTTMFYSNVLGMKVTTFKGDRKALCFGDQKFNLH |
| T...QSW..S....SPS.C.I.RL.H..V.T.K.IKD..MFYS.........FK...K.LC..DQ.F.L. | |
| Retrocopy | TPRIQSWSYS----SPSSCFIHRLNHM<VKTEKNIKDFCMFYSKIMHTETLAFKRNCKVLCLRDQIFDLR |
| Parental | EMGK-EFEPKAIHPLPGSLDICLITEAPLEEMIQRLKAFDVPIEEGPVPRTGAKGPIMSIYFRDPDRNLI |
| ..GK.E.EPKAIHPL....DICLITE.PL.E.I..L.AF....E.....RTGAKGPIMSI.F....RNLI | |
| Retrocopy | *RGK<EIEPKAIHPLCSYTDICLITEMPL-EII*HLQAFGDLNENCSFLRTGAKGPIMSICF*VTYRNLI |
| Parental | EVSNYIS |
| ..SNY.S | |
| Retrocopy | VLSNYLS |
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 | 2 .47 RPM |
| SRP017611_kidney | 0 .00 RPM | 48 .68 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .01 RPM |
| SRP040447_lung | 0 .00 RPM | 1 .24 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 0 .67 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_399 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_399 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 | ENSCPOG00000003997 | 1 retrocopy |
retro_cpor_399 ,
|