RetrogeneDB ID: | retro_cjac_2908 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:85575834..85576427(+) | ||
| Located in intron of: | ENSCJAG00000021555 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | WBSCR22 | ||
| Ensembl ID: | ENSCJAG00000016799 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2908
GAGCATGGCAGACCCCTGGAGCTGTTTTATGACAAGAAAAAAAAAAAAGCCTGGAAATACATTCCCAACTCACAGATGCT
TTGATTTCCAGATCAGGATGGCTGGGCGAGCATTGGAGCTTCTTTATCTGCCAGAGAATAAGCCCTGTTACCTGCTGGAT
ACTGGCTGTGGCACTGGGCTGAGTGAAGGTTCTCTCTCAGATGAAGGGCACTATTGGGTGGGCCTGGATATCAGCCCTGC
CATGCAGTATAAGGCCGTGGACTGAGATATAGAGGGAGACCTGCTTTTGGGGGACATGGGCCAGGGCATCCATTTCAAGC
TAGGCATATCTGATGGTTGCAGCAGCATTTCTGCTGTGCAGTGGTTCTGTAATGCTAACAAGAAATCTGAATATCCTGTC
AAGCACCTGTACTGCTTTTTAGCTTCTCTTTTTTCTGTTCTTGTCCAGGGATCCCAAGCTGTCTTGCAGCTATAACCTGA
GAACTCAGAGCTTGTAGGGGCTGATCACAACACAGGCGACAAAGGCGGGCTCCTCCGGTGGCATGGTGGTAGACTACCCC
GCCAGTGCCAAAGGAAAGAAGTTCTACCTCTGC
ORF - retro_cjac_2908 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.64 % |
| Parental protein coverage: | 68.88 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | EHGGPPELFYDKKEAR--KYVSNSRMI-EIQTRMAGRALELLCLPRNKPCYLLDIGCGTGLSGGYLSNEG |
| EHG.P.ELFYDKK.....KY..NS.M....Q.RMAGRALELL.LP.NKPCYLLD.GCGTGLS.G.LS.EG | |
| Retrocopy | EHGRPLELFYDKKKKKAWKYIPNSQML>DFQIRMAGRALELLYLPENKPCYLLDTGCGTGLSEGSLSDEG |
| Parental | HCWVGLDISPAMLDVDEAVDREVEGDLLLGDMGQGIPFKPGTFDGCISISAVQWLCNANKKSENPVKRLY |
| H.WVGLDISPAM.....AVD...EGDLLLGDMGQGI.FK.G..DGC.SISAVQW.CNANKKSE.PVK.LY | |
| Retrocopy | HYWVGLDISPAMQY--KAVD*DIEGDLLLGDMGQGIHFKLGISDGCSSISAVQWFCNANKKSEYPVKHLY |
| Parental | CFFASLFSVLVRGSRAVLQLYPENSEQL-ELITAQAMRAGFSGGVVVDYPNSARAKEAFLC |
| CF.ASLFSVLV.GS.AVLQL.PENSE....LIT.QA..AG.SGG.VVDYP.SA..K...LC | |
| Retrocopy | CFLASLFSVLVQGSQAVLQL*PENSELV>GLITTQATKAGSSGGMVVDYPASAKGKKFYLC |
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 .38 RPM | 8 .81 RPM |
| SRP051959_heart | 0 .61 RPM | 5 .51 RPM |
| SRP051959_kidney | 0 .95 RPM | 13 .82 RPM |
| SRP051959_liver | 0 .39 RPM | 7 .04 RPM |
| SRP051959_lung | 0 .54 RPM | 6 .72 RPM |
| SRP051959_lymph_node | 0 .84 RPM | 5 .27 RPM |
| SRP051959_skeletal_muscle | 0 .61 RPM | 9 .26 RPM |
| SRP051959_spleen | 0 .76 RPM | 6 .18 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2908 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2908 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2908 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016799 | 1 retrocopy |
retro_cjac_2908 ,
|
| Echinops telfairi | ENSETEG00000008874 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000017297 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000007038 | 1 retrocopy |