General information for g4246.t4
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.t4 | isoform | g4246.t4 | 605739 | 608312 |
| chr_2 | g4246 | g4246.t4 | exon | g4246.t4.exon1 | 605739 | 605971 |
| chr_2 | g4246 | g4246.t4 | exon | g4246.t4.exon2 | 606378 | 606558 |
| chr_2 | g4246 | g4246.t4 | exon | g4246.t4.exon3 | 606744 | 606932 |
| chr_2 | g4246 | g4246.t4 | cds | g4246.t4.CDS1 | 606873 | 606932 |
| chr_2 | g4246 | g4246.t4 | exon | g4246.t4.exon4 | 607357 | 607490 |
| chr_2 | g4246 | g4246.t4 | cds | g4246.t4.CDS2 | 607357 | 607490 |
| chr_2 | g4246 | g4246.t4 | exon | g4246.t4.exon5 | 607559 | 608312 |
| chr_2 | g4246 | g4246.t4 | cds | g4246.t4.CDS3 | 607559 | 607796 |
| chr_2 | g4246 | g4246.t4 | TTS | g4246.t4 | 608307 | 608307 |
| chr_2 | g4246 | g4246.t4 | TSS | g4246.t4 | NA | NA |
Sequences
>g4246.t4 Gene=g4246 Length=1491
AGCACTAAAAGTATTATTTTATATTTGCAAAAAAATAACATTAAATTAATTTTATATCAT
TCATTTATTCTTAATTTAGATTAATTAGATTATTAAATTAAATCTTTATTTACAAAATTA
TTAAGTTTAACAGTAGTCTAAAATTCAAATTTTTTTAGCAGTAATTTTTCTTAGTTGGAA
AATTTTTGTTCATTTTGGACAAGTCATTTTGTAAAAAAAATATTAAATTTGTAATAATAC
ACGATAAAATATAGAAAAAATGAGCGATAGTAATTCGACAGATAATGAAAATCAGCCGCG
TGGAATTGAAGCAGTCAAGAATCACATGCTAGAAAATAAGATCGAAACTGCATTATGGCT
TTCGAGAGTTCTATCAATAGTATTTGCAATCGGCTATCTTATTCCTATTTTTGGATCATC
TCAAAGTGCGTTTTATAAAGTATTAATTGCTAATGCAATCACAAGCGCCCTTCGATTACA
CCAACGATTGCCGCAAATTCAATTTACAAAGGAATTCTTAGCATTGCTTTTGATAGAGGA
TTCATGTCATTATCTATTTTTTTCACTGATATTCCTCTATGTGCAGCCTGTTCTCTTAGT
TTTTTACTCGGTCAAAACTCTTGGTGGGGTGCGAGATTATTGATTTCACTTGTAGAATTT
CAACAAAGAAACATTTTGAGATTGATTGCCTTTTCAGAAATTTTCTTAATGCCTGTCGCA
ATAATCTCAACATTTACTGGTCGTGCTGGTCTTATGACACCATTCATTTATTATCATTTT
TTGACTCTTCGTTATTCATCTCGTCGTAATCCACATACCCGAAATATGTTCCACGAACTG
AGATTGGCAACAGAAAATATTGCAAATAATCCTAAAGCACCTCCAATTATTGGAAAAGTA
TTGCATGGAGCTGTTAGATTGATTTCACGCCTTGCTCCGGCTCAAATACCACCACAACAA
CAACACGCCCAGTAAAATATTTTTCCTTCAAAAAAGTTTTTTTTAATTATTTAACGGGTT
TAATTCTGTTTCGTCTTATTTGGTAAAATGGATCATTTTTTTGTAGTGTTTTTTTCTATT
TTATTATAATACATTATATATTATTGATAAACATATTTTAATGTCATCATAATATGTTTA
ATTAGAGTTTTTTGCGGTATTAAATTTTAATATTACTCGTCTCTTGTGAATTATTCACAT
ACATACATAAAAAATTTTTCGTTGACATGCACATACATAAAACTTACATATATATATATA
TTGAAGAAATAGTAACAATTGTTTAAACAATTTAATTCAGAAACAAAAATTGTTTCAAAA
ATAAAAGACAAACGTGAATGTTTTGAAATAATTTGCATCAATTGAAATTTTTGTTTCCCA
ATAAATATTTGTTTTTATACTCTTATTCACAATTTGTTTTTTAATGTGCAATTGTAATAA
AATTTCAATTTATCAAATAAAAATTTTCAAAAAAATACTCTTAATTAAATG
>g4246.t4 Gene=g4246 Length=143
MSLSIFFTDIPLCAACSLSFLLGQNSWWGARLLISLVEFQQRNILRLIAFSEIFLMPVAI
ISTFTGRAGLMTPFIYYHFLTLRYSSRRNPHTRNMFHELRLATENIANNPKAPPIIGKVL
HGAVRLISRLAPAQIPPQQQHAQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4246.t4 | PANTHER | PTHR12703:SF4 | TRANSMEMBRANE PROTEIN 33 | 23 | 141 | 1.1E-26 |
| 3 | g4246.t4 | PANTHER | PTHR12703 | TRANSMEMBRANE PROTEIN 33 | 23 | 141 | 1.1E-26 |
| 1 | g4246.t4 | Pfam | PF03661 | Transmembrane protein 33/Nucleoporin POM33 | 21 | 132 | 1.8E-45 |
| 8 | g4246.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 11 | g4246.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 23 | - |
| 6 | g4246.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 24 | 43 | - |
| 12 | g4246.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 44 | 62 | - |
| 9 | g4246.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 63 | 67 | - |
| 10 | g4246.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 85 | - |
| 7 | g4246.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 86 | 143 | - |
| 4 | g4246.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 23 | - |
| 5 | g4246.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 44 | 66 | - |
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. There were no conditions that were differentially expressed