RetrogeneDB ID: | retro_cjac_1247 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 14:6714070..6714418(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000022737 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DYNLT3 | ||
| Ensembl ID: | ENSCJAG00000005227 | ||
| Aliases: | None | ||
| Description: | dynein, light chain, Tctex-type 3 [Source:HGNC Symbol;Acc:11694] |
Retrocopy-Parental alignment summary:
>retro_cjac_1247
GAGCAGTACCATCACCACTGCAATGAGGTTGCTTTCAATGCCGAGGAAGCCCACAATATTGTCAAAGAGTGTGTAGATGG
GGTTTTAAGTAGTGAAGATGATAATCACAACATTAACCAGTGGACCGCAAACATAGTGGAACAATCCTTAACACATCTGG
TTAAGTTGGGAAAAGCTTACAAAAATACTGTGACCTGTGCAGTGGTCCAGAATAGTGCATATGGCTTTCACACAGCCAGC
TCTGGTTTTTGGGATACCACACCTGATGGAACCTGTACCATAAGATGGGAGAACCAGACCCATCTTATGAAATGCACTGT
AAACGTTTTTACCATCACTATTGTTCTT
ORF - retro_cjac_1247 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.2 % |
| Parental protein coverage: | 99.14 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EEYHRHCDEVGFNAEEAHNIVKECVDGVLGGEDYNHNNINQWTASIVEQSLTHLVKLGKAYKYIVTCAVV |
| E.YH.HC.EV.FNAEEAHNIVKECVDGVL..ED.NHN.INQWTA.IVEQSLTHLVKLGKAYK..VTCAVV | |
| Retrocopy | EQYHHHCNEVAFNAEEAHNIVKECVDGVLSSEDDNHN-INQWTANIVEQSLTHLVKLGKAYKNTVTCAVV |
| Parental | QKSAYGFHTASSCFWDTTSDGTCTVRWENRT--MNCIVNVFAIAIVL |
| Q.SAYGFHTASS.FWDTT.DGTCT.RWEN.T..M.C.VNVF.I.IVL | |
| Retrocopy | QNSAYGFHTASSGFWDTTPDGTCTIRWENQTHLMKCTVNVFTITIVL |
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 | 10 .52 RPM |
| SRP051959_heart | 0 .00 RPM | 11 .14 RPM |
| SRP051959_kidney | 0 .00 RPM | 13 .69 RPM |
| SRP051959_liver | 0 .02 RPM | 6 .78 RPM |
| SRP051959_lung | 0 .02 RPM | 12 .95 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .30 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .31 RPM |
| SRP051959_spleen | 0 .00 RPM | 9 .81 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1247 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1247 was not experimentally validated.