RetrogeneDB ID: | retro_cjac_1865 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:160325417..160326101(+) | ||
| Located in intron of: | ENSCJAG00000001269 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000001275 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PGRMC2 | ||
| Ensembl ID: | ENSCJAG00000003328 | ||
| Aliases: | None | ||
| Description: | progesterone receptor membrane component 2 [Source:HGNC Symbol;Acc:16089] |
Retrocopy-Parental alignment summary:
>retro_cjac_1865
TGGCGGGCAATGATGGCGGCGGGTGATGGGGACGTGAAGCTAGGCACCCTGGGGAGTGGCAGCGAGAGCAGTAGCAACGC
CAGCCACCAGAGCCCCGGTGGCGTGGGAGTGTCAGCGGAAGGGGGAGGCTGGGCGGCGGCCGCGGCATTGGCTATTCTGA
CCGGCGGGGGCGGGGACATGCTGCTGAATGTGGCGCTGGTGCTGATGGGGGCCTACTGGGTGTGGGTGCGATGGGGGGGC
GGGGTATGGGGTCTGGGTCCGGGGCGGGGCGGGCGAGGAGACACCCGCCGCCTCTCTGCCTCACATTGGGAAGTGGGACT
TCAGCTTGGAGCAGCTGGGCCTGTATGACGGGTCCCGCAACCCGCTCATCCTGCTCTCGATCAGTGGGAAAAGTCTTCCA
TGTGACCAAAGGAAACAAGTTCTAAGGCCGGGCGGGTCCGTATGGAATATTTGCTGGGAGGGATGCCTCTAGAGGACTGG
CAACATTTTTGCCTAGATAAACATGCACTTAGAGAGGAATATGATGATCTCTCAGATTTGAATGCAGTACAAATGGAGAG
TGCTCGAGAATGGGAAATGCAGTTTAAAGAAAAATATGATGATGTAGGCAGACTCCTAAAACCAGGGGAAGAGTCATCAG
AATATACAGATGAGGACGATACCAAGGATCACAATAAACAGGAT
ORF - retro_cjac_1865 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.72 % |
| Parental protein coverage: | 91.53 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | WRAVMAAGDGDLKLGTLGSGSESSSDGSSESPGGAGAAAEGGGWAAAA-LALLTGGG-EMLLNVALVALV |
| WRA.MAAGDGD.KLGTLGSGSESSS..S..SPGG.G..AEGGGWAAAA.LA.LTGGG..MLLN...VALV | |
| Retrocopy | WRAMMAAGDGDVKLGTLGSGSESSSNASHQSPGGVGVSAEGGGWAAAAALAILTGGGGDMLLN---VALV |
| Parental | LLGAYRLWVRW-GRRGLGA--GAG-AGEESPAASLPRMKKRDFSLEQLRQYDGSRNPRILLAVNGK-VFD |
| L.GAY..WVRW.G.RG.G...GAG.AGEE.PAASLP...K.DFSLEQL..YDGSRNP.ILL...GK.VF. | |
| Retrocopy | LMGAYWVWVRW<GGRGMGSGSGAG<AGEETPAASLPHIGKWDFSLEQLGLYDGSRNPLILLSISGK>VFH |
| Parental | VTKGSKFYGPAGPYGIFAGRDASRGLATF-CLDKDALRDEYDDLSELNAVQMESVREWEMQFKEKYDYVG |
| VTKG.KF.G.AGPYGIFAGRDASRGLATF.CLDK.ALR.EYDDLS.LNAVQMES.REWEMQFKEKYD.VG | |
| Retrocopy | VTKGNKF*GRAGPYGIFAGRDASRGLATF>CLDKHALREEYDDLSDLNAVQMESAREWEMQFKEKYDDVG |
| Parental | RLLKPGEEPSEYTDEEDTKDHNKQD |
| RLLKPGEE.SEYTDE.DTKDHNKQD | |
| Retrocopy | RLLKPGEESSEYTDEDDTKDHNKQD |
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 |
|---|---|---|
| SRP051959_colon | 0 .07 RPM | 7 .01 RPM |
| SRP051959_heart | 0 .05 RPM | 23 .56 RPM |
| SRP051959_kidney | 0 .09 RPM | 20 .06 RPM |
| SRP051959_liver | 0 .06 RPM | 18 .09 RPM |
| SRP051959_lung | 0 .34 RPM | 10 .22 RPM |
| SRP051959_lymph_node | 0 .27 RPM | 8 .58 RPM |
| SRP051959_skeletal_muscle | 0 .04 RPM | 8 .19 RPM |
| SRP051959_spleen | 0 .06 RPM | 10 .17 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1865 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1865 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1865 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000003328 | 1 retrocopy |
retro_cjac_1865 ,
|
| Gorilla gorilla | ENSGGOG00000026492 | 1 retrocopy | |
| Procavia capensis | ENSPCAG00000002433 | 1 retrocopy |