RetrogeneDB ID: | retro_cpor_308 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_12:41132954..41133445(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C21ORF91 | ||
| Ensembl ID: | ENSCPOG00000012714 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_308
AAGCCAGATGAAAAATTACTCCCACAGTTTGATTCCGAAGTACCAAAATATTCTGCAAGATGGTTAGATAGAAGTACTAG
TGGCATCTCAAACTGTACACAATGAATTTTGAAGCAGATAAAAAATACAGACCTTGGACTTGCTATGTTACAAGGTCTAG
GTGCCACTTTACGCCATGACAGTGTTTTGTGGTCTCGTACTCACAGCCAGACACAGAAAAAAGAAGTGGCCATTTTCTTC
CCTGAAGCTTATGTCCAAATTCAGACTCTGCATTTACAGCAGAGAGGAATTGAACTGAATGATCTTGATGAAGTAGAACT
GAATATAAAATTTTGACAGCAAATCAGGAAGTTTTTGAAGAGTTAATACATCAAATACACGAAAAAGATTCTCTGACATC
ACAGTGTTGAGTCCACCACGTTGCCACTGAACAGCTTCACAAGAACTGCTCCAAGTTACCATGCCTGTAAGTAGGACAAA
CAGAAGCAAAC
ORF - retro_cpor_308 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.05 % |
| Parental protein coverage: | 54.39 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | KPDKKLLPQFDSQVPKYSARWIDGSTSGISNCTQEILEQRKNTDFGLAVLQGPGAALCHDNVLW--PHAQ |
| KPD.KLLPQFDS.VPKYSARW.D.STSGISNCTQ.IL.Q.KNTD.GLA.LQG.GA.L.HD.VLW...H.Q | |
| Retrocopy | KPDEKLLPQFDSEVPKYSARWLDRSTSGISNCTQ*ILKQIKNTDLGLAMLQGLGATLRHDSVLWSRTHSQ |
| Parental | GQ--EEATFCPEANVPTQTLR-YSREELNSM-TLDEVKQLNTKLRQQI-QDVFEELTHQVQEKDSLISER |
| .Q..E.A.F.PEA.V..QTL..YSREELN.M..LDEV..LN.K..QQI.Q.VFEEL.HQ..EKDSL.S.. | |
| Retrocopy | TQKKEVAIFFPEAYVQIQTLH>YSREELN*M<DLDEV-ELNIKF*QQI<QEVFEELIHQIHEKDSLTSQC |
| Parental | HGRHVAIEQLHKNCSKLPCLQVGRTGTN |
| ...HVA.EQLHKNCSKLPCL.VG.T..N | |
| Retrocopy | *VHHVATEQLHKNCSKLPCL*VGQTEAN |
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 | 4 .20 RPM |
| SRP017611_kidney | 0 .00 RPM | 1 .36 RPM |
| SRP017611_liver | 0 .00 RPM | 3 .40 RPM |
| SRP040447_lung | 0 .00 RPM | 3 .05 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 1 .15 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_308 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_308 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 | ENSCPOG00000012714 | 1 retrocopy |
retro_cpor_308 ,
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