RetrogeneDB ID: | retro_cjac_2439 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:54292263..54292672(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SARNP | ||
| Ensembl ID: | ENSCJAG00000007853 | ||
| Aliases: | None | ||
| Description: | SAP domain containing ribonucleoprotein [Source:HGNC Symbol;Acc:24432] |
Retrocopy-Parental alignment summary:
>retro_cjac_2439
GGTTTGGAGACCAAGGGAATAAAGCAAGATCTTATCCACAGACTCCAGGCATATCTTGAAGAATATGCTGAAGAGGCAGC
CAATGAAGATGATGTACTGGGAGATGAAACAGAGGAAGAAGAAACAAAGCTCATGGAGCTCCCTATCAAAGAGGAAGAAC
CCCTTGAAAAAAACTGTTGATGTGGCAGCACAGAAGAAAGTGGTGAAAATTACATCTGAAATACTACAGACTGAGAGAAT
GCGAAAGAGAGCCAAACGAGTCAATGTACCTGTGAGCTTGGAGAGCAAGAAAGTTGCTCAGGCAGCTAAGTTTGGGATTT
CTTCACTTCCAACAAAAGAGCTGTCATCTGATAACAAACCTATGGTTAACTTGGATAAGCTGAAGCAAAGAGCTCGAATC
TTTGAACTC
ORF - retro_cjac_2439 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.48 % |
| Parental protein coverage: | 64.76 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GLETKGIKQDLIHRLQAYLEEHAEEEANEEDVLGDETEEEETKPIELPVKEEEPPEK-TVDVAAEKKVVK |
| GLETKGIKQDLIHRLQAYLEE.AEE.ANE.DVLGDETEEEETK..ELP.KEEEP.EK.TVDVAA.KKVVK | |
| Retrocopy | GLETKGIKQDLIHRLQAYLEEYAEEAANEDDVLGDETEEEETKLMELPIKEEEPLEK>TVDVAAQKKVVK |
| Parental | ITSEIPQTERMQKRAERFNVPVSLESKKAARAARFGISSVPTKGLPSDNKPMVSLDKLKERAQRFGL |
| ITSEI.QTERM.KRA.R.NVPVSLESKK.A.AA.FGISS.PTK.L.SDNKPMV.LDKLK.RA..F.L | |
| Retrocopy | ITSEILQTERMRKRAKRVNVPVSLESKKVAQAAKFGISSLPTKELSSDNKPMVNLDKLKQRARIFEL |
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 .13 RPM | 14 .29 RPM |
| SRP051959_heart | 0 .16 RPM | 16 .98 RPM |
| SRP051959_kidney | 0 .24 RPM | 18 .99 RPM |
| SRP051959_liver | 0 .13 RPM | 12 .97 RPM |
| SRP051959_lung | 0 .15 RPM | 19 .13 RPM |
| SRP051959_lymph_node | 0 .23 RPM | 21 .78 RPM |
| SRP051959_skeletal_muscle | 0 .33 RPM | 17 .54 RPM |
| SRP051959_spleen | 0 .27 RPM | 21 .03 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2439 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2439 was not experimentally validated.