General information for g4246.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g4246.t1 | 605910 | 605910 |
| chr_2 | g4246 | g4246.t1 | isoform | g4246.t1 | 606404 | 607796 |
| chr_2 | g4246 | g4246.t1 | exon | g4246.t1.exon1 | 606404 | 606558 |
| chr_2 | g4246 | g4246.t1 | cds | g4246.t1.CDS1 | 606404 | 606558 |
| chr_2 | g4246 | g4246.t1 | exon | g4246.t1.exon2 | 606744 | 606993 |
| chr_2 | g4246 | g4246.t1 | cds | g4246.t1.CDS2 | 606744 | 606993 |
| chr_2 | g4246 | g4246.t1 | exon | g4246.t1.exon3 | 607357 | 607490 |
| chr_2 | g4246 | g4246.t1 | cds | g4246.t1.CDS3 | 607357 | 607490 |
| chr_2 | g4246 | g4246.t1 | exon | g4246.t1.exon4 | 607559 | 607796 |
| chr_2 | g4246 | g4246.t1 | cds | g4246.t1.CDS4 | 607559 | 607796 |
| chr_2 | g4246 | g4246.t1 | TTS | g4246.t1 | 608224 | 608224 |
Sequences
>g4246.t1 Gene=g4246 Length=777
ATGAGCGATAGTAATTCGACAGATAATGAAAATCAGCCGCGTGGAATTGAAGCAGTCAAG
AATCACATGCTAGAAAATAAGATCGAAACTGCATTATGGCTTTCGAGAGTTCTATCAATA
GTATTTGCAATCGGCTATCTTATTCCTATTTTTGGATCATCTCAAAGTGCGTTTTATAAA
GTATTAATTGCTAATGCAATCACAAGCGCCCTTCGATTACACCAACGATTGCCGCAAATT
CAATTTACAAAGGAATTCTTAGCATTGCTTTTGATAGAGGATTCATGTCATTATCTATTT
TTTTCACTGATATTCCTCTATGTGCAGCCTGTTCTCTTAGTTTTGTTCCCAGTAGTTCTT
TTTGCCGTTCTTCATTCAGCGAGTTACTCATTAAAAATGCTTGATTTACTCGGTCAAAAC
TCTTGGTGGGGTGCGAGATTATTGATTTCACTTGTAGAATTTCAACAAAGAAACATTTTG
AGATTGATTGCCTTTTCAGAAATTTTCTTAATGCCTGTCGCAATAATCTCAACATTTACT
GGTCGTGCTGGTCTTATGACACCATTCATTTATTATCATTTTTTGACTCTTCGTTATTCA
TCTCGTCGTAATCCACATACCCGAAATATGTTCCACGAACTGAGATTGGCAACAGAAAAT
ATTGCAAATAATCCTAAAGCACCTCCAATTATTGGAAAAGTATTGCATGGAGCTGTTAGA
TTGATTTCACGCCTTGCTCCGGCTCAAATACCACCACAACAACAACACGCCCAGTAA
>g4246.t1 Gene=g4246 Length=258
MSDSNSTDNENQPRGIEAVKNHMLENKIETALWLSRVLSIVFAIGYLIPIFGSSQSAFYK
VLIANAITSALRLHQRLPQIQFTKEFLALLLIEDSCHYLFFSLIFLYVQPVLLVLFPVVL
FAVLHSASYSLKMLDLLGQNSWWGARLLISLVEFQQRNILRLIAFSEIFLMPVAIISTFT
GRAGLMTPFIYYHFLTLRYSSRRNPHTRNMFHELRLATENIANNPKAPPIIGKVLHGAVR
LISRLAPAQIPPQQQHAQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4246.t1 | PANTHER | PTHR12703:SF4 | TRANSMEMBRANE PROTEIN 33 | 3 | 256 | 4.4E-65 |
| 3 | g4246.t1 | PANTHER | PTHR12703 | TRANSMEMBRANE PROTEIN 33 | 3 | 256 | 4.4E-65 |
| 1 | g4246.t1 | Pfam | PF03661 | Transmembrane protein 33/Nucleoporin POM33 | 12 | 247 | 2.4E-99 |
| 10 | g4246.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 29 | - |
| 14 | g4246.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 30 | 51 | - |
| 11 | g4246.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 52 | 56 | - |
| 17 | g4246.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 57 | 74 | - |
| 9 | g4246.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 75 | 85 | - |
| 19 | g4246.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 86 | 108 | - |
| 13 | g4246.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 109 | 113 | - |
| 18 | g4246.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 114 | 138 | - |
| 7 | g4246.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 139 | 158 | - |
| 16 | g4246.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 159 | 177 | - |
| 12 | g4246.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 178 | 182 | - |
| 15 | g4246.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 183 | 200 | - |
| 8 | g4246.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 201 | 258 | - |
| 4 | g4246.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 32 | 54 | - |
| 5 | g4246.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 103 | 125 | - |
| 6 | g4246.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 159 | 181 | - |
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 transcript has been annotated with K20724 (transmembrane protein 33)
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.
