RetrogeneDB ID: | retro_cjac_509 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:23611884..23612305(-) | ||
| Located in intron of: | ENSCJAG00000014666 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000001105 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_509
TGCAAAAGTGGTTTTCTTCTGGATGGCTTCCCTTGTACTGAGAGGCAGGCATAAATGCTTGATGACCTCATGGAGAAGAG
GAAAGAGAAACCTGATTCTGTGATTGAATTCAGCATCCCAGACTCTGCTGATCCAAAGAATCACAGGAAGGCTGATTCAC
CCCAAGAGTGGCCATTCCTGCCGTGAAGAGTTCAACCCCTCAAAGGAGCCCATGAAAGATAACATCACCAGGGAGCCCTT
GATTCATTGATCAAATGATAATGAGACAGCCTTGAAAATCTGCCTGCAAGCCTACCACACTCAAAGCACCCCACTCATGG
AGTACTACAGGAAATGGGGGATCCTCGCTGTCATCAATGCATCCCAGTCCCCTGATGTAGTGTTCACATGCATCCTAGCA
GCCTTCTCCAAAGCCACATCC
ORF - retro_cjac_509 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.58 % |
| Parental protein coverage: | 60.78 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | CKNGFLLDGFPRTVRQAEMLDDLMEKRKEKLDSVIEFSIPDS-LLIRRITGRLIHPKSGRSYHEEFNPPK |
| CK.GFLLDGFP.T.RQA.MLDDLMEKRKEK.DSVIEFSIPDS.L..R.ITGRLIHPKSG.S..EEFNP.K | |
| Retrocopy | CKSGFLLDGFPCTERQA*MLDDLMEKRKEKPDSVIEFSIPDS>LIQR-ITGRLIHPKSGHSCREEFNPSK |
| Parental | EPMKDDITGEPLIRRSDDNEKALKIRLQAYHTQTTPLIEYYRKRGIHSAIDASQTPDVVFACILAAFSKA |
| EPMKD.IT.EPLI..S.DNE.ALKI.LQAYHTQ.TPL.EYYRK.GI...I.ASQ.PDVVF.CILAAFSKA | |
| Retrocopy | EPMKDNITREPLIH*SNDNETALKICLQAYHTQSTPLMEYYRKWGILAVINASQSPDVVFTCILAAFSKA |
| Parental | TS |
| TS | |
| Retrocopy | TS |
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 .02 RPM | 32 .50 RPM |
| SRP051959_heart | 0 .02 RPM | 21 .61 RPM |
| SRP051959_kidney | 0 .04 RPM | 40 .31 RPM |
| SRP051959_liver | 0 .04 RPM | 45 .12 RPM |
| SRP051959_lung | 0 .02 RPM | 25 .56 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 25 .66 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 18 .10 RPM |
| SRP051959_spleen | 0 .02 RPM | 29 .58 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_509 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_509 was not experimentally validated.