RetrogeneDB ID: | retro_cjac_3111 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 8:12041545..12041904(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSCJAG00000012353 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | RPA3 | ||
| Ensembl ID: | ENSCJAG00000000705 | ||
| Aliases: | None | ||
| Description: | replication protein A3, 14kDa [Source:HGNC Symbol;Acc:10291] |
Retrocopy-Parental alignment summary:
>retro_cjac_3111
GTGGACATGATGGAGGCGCCCAGGTTGCGCCTCAACACCGGCAGCTGACTCAGTTCATCGACAAGCCTGTCTGCTTCATA
GGGAAGCTGGAAAAGATTCATCCCACCAGAAAAACGTTTATTCTTTCAGATGAGGAAGGAAAATATGGAACCATTGAGTT
GATGGAACCCCTTGACGAAGAAATATCTGGAATTATGGAAGTGGTTGGAAAAGTAACTGCCAAGATGACCATCATGGGTA
CATCTTATGTCCAGTTTAAAGAAGATAACCAACCTTTTGACCTTGGACTTTACAATGAAGCTGTGAAAATGAACCATCAG
TTCCCTCAGTTTTATCCTTTAGGGATTATGCAACATGAT
GTGGACATGATGGAGGCGCCCAGGTTGCGCCTCAACACCGGCAGCTGACTCAGTTCATCGACAAGCCTGTCTGCTTCATA
GGGAAGCTGGAAAAGATTCATCCCACCAGAAAAACGTTTATTCTTTCAGATGAGGAAGGAAAATATGGAACCATTGAGTT
GATGGAACCCCTTGACGAAGAAATATCTGGAATTATGGAAGTGGTTGGAAAAGTAACTGCCAAGATGACCATCATGGGTA
CATCTTATGTCCAGTTTAAAGAAGATAACCAACCTTTTGACCTTGGACTTTACAATGAAGCTGTGAAAATGAACCATCAG
TTCCCTCAGTTTTATCCTTTAGGGATTATGCAACATGAT
ORF - retro_cjac_3111 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.99 % |
| Parental protein coverage: | 99.17 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VDMMELPRARMNVS-MLTQFIDKPVCFVGRLEKIHPTGKMFILSDGEGKNVTIELMEPLDEEISGIIEVV |
| VDMME.PR.R.N....LTQFIDKPVCF.G.LEKIHPT.K.FILSD.EGK..TIELMEPLDEEISGI.EVV | |
| Retrocopy | VDMMEAPRLRLNTG<QLTQFIDKPVCFIGKLEKIHPTRKTFILSDEEGKYGTIELMEPLDEEISGIMEVV |
| Parental | GKVTAKATIMCTSFVQFKEDNHPFDLGLYNEAVKIIHEFPQFYPLGIVQHD |
| GKVTAK.TIM.TS.VQFKEDN.PFDLGLYNEAVK..H.FPQFYPLGI.QHD | |
| Retrocopy | GKVTAKMTIMGTSYVQFKEDNQPFDLGLYNEAVKMNHQFPQFYPLGIMQHD |
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 | 4 .99 RPM |
| SRP051959_heart | 0 .00 RPM | 4 .40 RPM |
| SRP051959_kidney | 0 .00 RPM | 6 .23 RPM |
| SRP051959_liver | 0 .00 RPM | 6 .63 RPM |
| SRP051959_lung | 0 .00 RPM | 5 .51 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 6 .83 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .56 RPM |
| SRP051959_spleen | 0 .04 RPM | 6 .68 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3111 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3111 was not experimentally validated.