RetrogeneDB ID: | retro_cpor_1135 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_5:28112965..28113680(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | IKZF3 | ||
| Ensembl ID: | ENSCPOG00000005792 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1135
AAAGTTAAGGATGAACGTGGTAAAAAAGAGAAGAATATTGTAAGCCATTGCCCAGGGGAAATGTGCAAGAACCTGACATT
GCTTACAGCTATGCAAGGGAACATAATGCATATGAAACCATTAAGTTGGAGAGCCATCTCTCACATGATAATAACAAGCC
AATCAGTGGGAAGATAAGCTTCCATGCGTGTGAATTATCTTGTATTAGTTTCCATGTCTTAATGGTTTGTAAGTGGAGCC
ATATTGGTGAATGCCCTTTGTGGTGTAATTAGCATGGGGCATTTTTACTCAGAAAGGTAGACTCCTCCACCACAATACAC
TGCACAAAGAAAAAAATACTTTTAAAACCTGTGCATGCCAGTGGAGAGATGCATTCATGGGGCACCTTGGGAATCATTCT
GTGGAGAAGCCCAAAAAATGTGAGTTTGCAGGAGTTACAAGCAGAGAAGTTCCTGTGAGGAGCACATGGAGTACTGTTGC
ACATTTCTTCAGAGCTCTGACGTGCAGGACACAGCAAGAGCGAGACCAAACACATCAGAGCAGAAATGGGAAGTGACAGA
GCTCTGGTTCTGGACAGATTAGCAAGTAATGTGGCAAAACAAAAAAGCCCAATACTTCAGAAATTCATTGGTGAGAAGTG
CCACTGCTTTGGCACCAATTATAATTCCAGCTATGTGCAGGAGAAGGAAGAGAGATAAAACAGACCTGAATGATG
ORF - retro_cpor_1135 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.96 % |
| Parental protein coverage: | 53.83 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | KVKDEYSEREENVL-KPEPLGNMEEPEIPYSYAREYTEYDSIKLERHAAAYDSGRPAGGKMNCDVCGLSC |
| KVKDE....E.N...KP.P.GN..EP.I.YSYARE...Y..IKLE.H....D...P..GK.....C.LSC | |
| Retrocopy | KVKDERGKKEKNIV<KPLPRGNVQEPDIAYSYAREHNAYETIKLESHLS-HDNNKPISGKISFHACELSC |
| Parental | ISFNVLMVHKRSHTGERPFQCNQCGAS-FTQKGNLLRHIKLHTGEKPFKCHLCSYACQRRDALTGHLRTH |
| ISF.VLMV.K.SH.GE.P..CN..GA..FTQKG.LL.H..LH.....FK......ACQ.RDA..GHL..H | |
| Retrocopy | ISFHVLMVCKWSHIGECPLWCN*HGAF<FTQKGRLLHHNTLHKEKNTFK----TCACQWRDAFMGHLGNH |
| Parental | SVEKPYKCEF-CGRSYKQRSSLEEHKERCRTFLQSPDLGDTASA-EARHIKAEMGSERALVLDRLASNVA |
| SVEKP.KCEF.C.RSYKQRSS.EEH.E.C.TFLQS.D..DTA.A.E..HI.AEMGS.RALVLDRLASNVA | |
| Retrocopy | SVEKPKKCEF<C-RSYKQRSSCEEHMEYCCTFLQSSDVQDTARA<ETKHIRAEMGSDRALVLDRLASNVA |
| Parental | KRKSSMPQKFIGEKRHCFDVTYNSSYLYEKDS-EMMQTRMM |
| K.KS...QKFIGEK.HCF...YNSSY..EK...E..QT.MM | |
| Retrocopy | KQKSPILQKFIGEKCHCFGTNYNSSYVQEKEE<EIKQT*MM |
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 | 0 .00 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .42 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .09 RPM |
| SRP040447_lung | 0 .00 RPM | 4 .06 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 0 .01 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1135 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1135 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 | ENSCPOG00000005792 | 1 retrocopy |
retro_cpor_1135 ,
|
| Cavia porcellus | ENSCPOG00000021914 | 1 retrocopy |