General information for g4246.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Krueppel homolog 2.
Parent gene
- The parent gene g4246 is located on chr_2: 607620..608312 (+ 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_2 | g4246 | g4246.t16 | isoform | g4246.t16 | 606945 | 608220 |
| chr_2 | g4246 | g4246.t16 | exon | g4246.t16.exon1 | 606945 | 606993 |
| chr_2 | g4246 | g4246.t16 | cds | g4246.t16.CDS1 | 606985 | 606993 |
| chr_2 | g4246 | g4246.t16 | exon | g4246.t16.exon2 | 607357 | 607490 |
| chr_2 | g4246 | g4246.t16 | cds | g4246.t16.CDS2 | 607357 | 607490 |
| chr_2 | g4246 | g4246.t16 | exon | g4246.t16.exon3 | 607559 | 608220 |
| chr_2 | g4246 | g4246.t16 | cds | g4246.t16.CDS3 | 607559 | 607796 |
| chr_2 | g4246 | g4246.t16 | TTS | g4246.t16 | 608224 | 608224 |
| chr_2 | g4246 | g4246.t16 | TSS | g4246.t16 | NA | NA |
Sequences
>g4246.t16 Gene=g4246 Length=845
TCTTTTTGCCGTTCTTCATTCAGCGAGTTACTCATTAAAAATGCTTGATTTACTCGGTCA
AAACTCTTGGTGGGGTGCGAGATTATTGATTTCACTTGTAGAATTTCAACAAAGAAACAT
TTTGAGATTGATTGCCTTTTCAGAAATTTTCTTAATGCCTGTCGCAATAATCTCAACATT
TACTGGTCGTGCTGGTCTTATGACACCATTCATTTATTATCATTTTTTGACTCTTCGTTA
TTCATCTCGTCGTAATCCACATACCCGAAATATGTTCCACGAACTGAGATTGGCAACAGA
AAATATTGCAAATAATCCTAAAGCACCTCCAATTATTGGAAAAGTATTGCATGGAGCTGT
TAGATTGATTTCACGCCTTGCTCCGGCTCAAATACCACCACAACAACAACACGCCCAGTA
AAATATTTTTCCTTCAAAAAAGTTTTTTTTAATTATTTAACGGGTTTAATTCTGTTTCGT
CTTATTTGGTAAAATGGATCATTTTTTTGTAGTGTTTTTTTCTATTTTATTATAATACAT
TATATATTATTGATAAACATATTTTAATGTCATCATAATATGTTTAATTAGAGTTTTTTG
CGGTATTAAATTTTAATATTACTCGTCTCTTGTGAATTATTCACATACATACATAAAAAA
TTTTTCGTTGACATGCACATACATAAAACTTACATATATATATATATTGAAGAAATAGTA
ACAATTGTTTAAACAATTTAATTCAGAAACAAAAATTGTTTCAAAAATAAAAGACAAACG
TGAATGTTTTGAAATAATTTGCATCAATTGAAATTTTTGTTTCCCAATAAATATTTGTTT
TTATA
>g4246.t16 Gene=g4246 Length=126
MLDLLGQNSWWGARLLISLVEFQQRNILRLIAFSEIFLMPVAIISTFTGRAGLMTPFIYY
HFLTLRYSSRRNPHTRNMFHELRLATENIANNPKAPPIIGKVLHGAVRLISRLAPAQIPP
QQQHAQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4246.t16 | PANTHER | PTHR12703:SF4 | TRANSMEMBRANE PROTEIN 33 | 3 | 124 | 4.6E-27 |
| 3 | g4246.t16 | PANTHER | PTHR12703 | TRANSMEMBRANE PROTEIN 33 | 3 | 124 | 4.6E-27 |
| 1 | g4246.t16 | Pfam | PF03661 | Transmembrane protein 33/Nucleoporin POM33 | 1 | 115 | 1.6E-46 |
| 6 | g4246.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 35 | - |
| 7 | g4246.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 36 | 62 | - |
| 5 | g4246.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 63 | 126 | - |
| 4 | g4246.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 41 | 63 | - |
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:0016021 | integral component of membrane | CC |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
