General information for g16841.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative RING-box protein 2.
Parent gene
- The parent gene g16841 is located on chr_4: 11365453..11366002 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_4 | g16841 | g16841.t1 | TTS | g16841.t1 | 11365394 | 11365394 |
| chr_4 | g16841 | g16841.t1 | isoform | g16841.t1 | 11365453 | 11366002 |
| chr_4 | g16841 | g16841.t1 | exon | g16841.t1.exon1 | 11365453 | 11365525 |
| chr_4 | g16841 | g16841.t1 | cds | g16841.t1.CDS1 | 11365453 | 11365525 |
| chr_4 | g16841 | g16841.t1 | exon | g16841.t1.exon2 | 11365585 | 11365630 |
| chr_4 | g16841 | g16841.t1 | cds | g16841.t1.CDS2 | 11365585 | 11365630 |
| chr_4 | g16841 | g16841.t1 | exon | g16841.t1.exon3 | 11365691 | 11365763 |
| chr_4 | g16841 | g16841.t1 | cds | g16841.t1.CDS3 | 11365691 | 11365763 |
| chr_4 | g16841 | g16841.t1 | exon | g16841.t1.exon4 | 11365865 | 11366002 |
| chr_4 | g16841 | g16841.t1 | cds | g16841.t1.CDS4 | 11365865 | 11366002 |
| chr_4 | g16841 | g16841.t1 | TSS | g16841.t1 | 11366146 | 11366146 |
Sequences
>g16841.t1 Gene=g16841 Length=330
ATGGATGAAGAAGATAAAATTTCTGATAGCGAAAATCAAACAAAACCAGAAAAAATGTTT
ACATTAAAAAGATGGAATAGTGTGGCTATGTGGTCATGGGATTGTTCAACAGATACTTGT
GCTATATGTCGAGTTCAAGTCATGGATGCATGTTTAAGATGTCAAGCAGAATCTAAAAAA
GATGCTACTAATAAAGATGTTACTTGTGTTGTTTGTTGGGGTGAATGCAATCACAGTTTC
CATCACTGCTGTATTAGTTTATGGGTGAAACAATCAAACAGATGTCCATTATGTCAACAA
GAATGGAGTATTCAACGACTGTCAAGTTAA
>g16841.t1 Gene=g16841 Length=109
MDEEDKISDSENQTKPEKMFTLKRWNSVAMWSWDCSTDTCAICRVQVMDACLRCQAESKK
DATNKDVTCVVCWGECNHSFHHCCISLWVKQSNRCPLCQQEWSIQRLSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g16841.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 7 | 109 | 0.00 |
| 2 | g16841.t1 | PANTHER | PTHR11210 | RING BOX | 6 | 107 | 0.00 |
| 3 | g16841.t1 | PANTHER | PTHR11210:SF27 | RING-BOX PROTEIN 2 | 6 | 107 | 0.00 |
| 1 | g16841.t1 | Pfam | PF12678 | RING-H2 zinc finger domain | 38 | 99 | 0.00 |
| 6 | g16841.t1 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 51 | 99 | 9.76 |
| 4 | g16841.t1 | SUPERFAMILY | SSF57850 | RING/U-box | 18 | 106 | 0.00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0008270 | zinc ion binding | MF |
KEGG
Orthology
- This transcript has been annotated with K10611 (RING-box protein 2)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
