RetrogeneDB ID: | retro_cjac_2580 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:150014692..150015174(+) | ||
| Located in intron of: | ENSCJAG00000018140 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000012116 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2580
ATGGACACCTTAGAAGAAAGCTTCACGGTGCCCTTCTCCTCTGACTCTGATGCACATTTTGATGCTGTGGTTGGATATTT
AGAAGACATTATCATGGATGAAGACTGCTAGTTATTACAGAGAAATTTCATGGACAACTACTACCAGGAGTTTGAGGACA
CCGAAGAGAATAAACTCACCTACACACCTATTTTTAATGAACATATTTCTTTGGCAGAAAAGTATATAGAAGAACAGTTG
CAAGAGCAAATTCTTAGCTTTAACATAGCAGCTTTCACAACATTACAGCATCACAAAGATGAAGTGATTGGTGACATCCT
CCAAACGTTGCTCACATTTACAGATTTTCTGGCTTTTAAAGCAAGGTTTCTGGGCTCCAGAGCAGAAAAAGAAGGTCAGG
GACTGGACTTAAGCTGTGGTTTAGTGGAGACTTCATTGGCAAATCATCTTCTATGTCATCTTCCCAGAATAATCTGCGAT
AC
ORF - retro_cjac_2580 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.46 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MDALEESFALSFSSASDAEFDAVVGYLEDIIMDDKFQLLQRNFMDKYYLEFEDTEENKLTYTPIFNEYIS |
| MD.LEESF...FSS.SDA.FDAVVGYLEDIIMD....LLQRNFMD.YY.EFEDTEENKLTYTPIFNE.IS | |
| Retrocopy | MDTLEESFTVPFSSDSDAHFDAVVGYLEDIIMDEDC*LLQRNFMDNYYQEFEDTEENKLTYTPIFNEHIS |
| Parental | LVEKYVEEQLLERIPGFNMAAFTVTLQHHRDEVAGDIFDMLLTFTDFLAFKEMFLDYRAEKEGRGLDLSS |
| L.EKY.EEQL.E.I..FN.AAFT.TLQHH.DEV.GDI...LLTFTDFLAFK..FL..RAEKEG.GLDLS. | |
| Retrocopy | LAEKYIEEQLQEQILSFNIAAFT-TLQHHKDEVIGDILQTLLTFTDFLAFKARFLGSRAEKEGQGLDLSC |
| Parental | GLVVTSLC-KSSSVPASPNNLRH |
| GLV.TSL..KSSS...S.NNLR. | |
| Retrocopy | GLVETSLA<KSSSMSSSQNNLRY |
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 | 5 .59 RPM |
| SRP051959_heart | 0 .00 RPM | 8 .37 RPM |
| SRP051959_kidney | 0 .04 RPM | 8 .39 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .86 RPM |
| SRP051959_lung | 0 .00 RPM | 11 .22 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 6 .89 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 4 .45 RPM |
| SRP051959_spleen | 0 .00 RPM | 5 .86 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2580 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2580 was not experimentally validated.