RetrogeneDB ID: | retro_cjac_138 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:165067411..165067834(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000021774 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000012432 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_138
ATGGACAGCCGGATTCCTTATGATGACTACCGGGTGGTTTTCTTGCCTGCCTATGAGAATCTGTTAGCATGGATTCCTCC
TTATAAGAGGTTATACCACGCAGACTACAACAATGAGTTGACCCAGTTTCTTCCCCAAACCATCACACGGAAGAAGCCTC
CTGGAGCTCAGATGGGATTTAACATCCGAGGAGGAAAGGCCTCCCAGCTAGGCATCTTCATCTCCAAGGTAATTCCTGAC
TCTGATGCACATAGAGCAGGACCTCAGGAAGGGGACCAAGTTCTAGCTGTGAATGATGTGGATTTCCAAGATACTGAGCA
CAGCAAGGCTGTTGAGATCCTGAAGACAGCTTGTGAAATCAGCATGCGTGTCCGCTTCTTTACCTACAATTATCATCTCC
AAAAGGAGCAGACTGTGCACTAG
ORF - retro_cjac_138 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.86 % |
| Parental protein coverage: | 81.87 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MDSRIPYDDYPVVFLPAYENPPAWIPPHERVHHPDYNNELTQFLPRTITLKKPPGAQLGFNIRGGKASQL |
| MDSRIPYDDY.VVFLPAYEN..AWIPP..R..H.DYNNELTQFLP.TIT.KKPPGAQ.GFNIRGGKASQL | |
| Retrocopy | MDSRIPYDDYRVVFLPAYENLLAWIPPYKRLYHADYNNELTQFLPQTITRKKPPGAQMGFNIRGGKASQL |
| Parental | GIFISKVIPDSDAHRAGLQEGDQVLAVNDVDFQDIEHSKAVEILKTAREISMRVRFFPYNYHRQKERTVH |
| GIFISKVIPDSDAHRAG.QEGDQVLAVNDVDFQD.EHSKAVEILKTA.EISMRVRFF.YNYH.QKE.TVH | |
| Retrocopy | GIFISKVIPDSDAHRAGPQEGDQVLAVNDVDFQDTEHSKAVEILKTACEISMRVRFFTYNYHLQKEQTVH |
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 .00 RPM | 6 .48 RPM |
| SRP051959_heart | 0 .00 RPM | 6 .28 RPM |
| SRP051959_kidney | 0 .02 RPM | 8 .05 RPM |
| SRP051959_liver | 0 .06 RPM | 6 .48 RPM |
| SRP051959_lung | 0 .02 RPM | 6 .60 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 6 .35 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 4 .19 RPM |
| SRP051959_spleen | 0 .06 RPM | 8 .24 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_138 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_138 was not experimentally validated.