General information for g1223.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g1223 is located on chr_3: 8903244..8903769 (+ 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_3 | g1223 | g1223.t1 | TSS | g1223.t1 | 8903198 | 8903198 |
| chr_3 | g1223 | g1223.t1 | isoform | g1223.t1 | 8903244 | 8903769 |
| chr_3 | g1223 | g1223.t1 | exon | g1223.t1.exon1 | 8903244 | 8903346 |
| chr_3 | g1223 | g1223.t1 | cds | g1223.t1.CDS1 | 8903244 | 8903346 |
| chr_3 | g1223 | g1223.t1 | exon | g1223.t1.exon2 | 8903405 | 8903769 |
| chr_3 | g1223 | g1223.t1 | cds | g1223.t1.CDS2 | 8903405 | 8903769 |
| chr_3 | g1223 | g1223.t1 | TTS | g1223.t1 | 8903792 | 8903792 |
Sequences
>g1223.t1 Gene=g1223 Length=468
ATGAATAGACAAATATTTTTGATCATTTGTTCTTCTCTTTTACTATCAGCTTCTGCTGAA
TTTATTGCAATTCCATATGGATCATGTGGTGAAGGTTTTGAAGATCTAAGTTGTACAATT
GAAAGTGTAACAGTTCAAGAGTGTGACATAATAGAGAAAAAGTTTTGTGAATTAATCAGA
GGTGAATCTTATCAAATGAATATGACATTCATACCACAATTTGAAGGCAGTGACTTGTCA
TTAAAAGCATATGCAATAATTAATGGAAAAGAACTACCATTTGAAGAAATGAATAGCAAA
GCATGTGATTATATGGAATGTCCTATTAAAAAAGGAGTACAACAAGATTATGTTTTTAAT
GTCAATGTTGATATGCTGAAACCACGTGGAAAATTCAATGTTCGATGGCTGATGAAGCAA
GGAAATGAAAATCGATGCTGTTTTACTAATAAATTTAAAATTGCCTAA
>g1223.t1 Gene=g1223 Length=155
MNRQIFLIICSSLLLSASAEFIAIPYGSCGEGFEDLSCTIESVTVQECDIIEKKFCELIR
GESYQMNMTFIPQFEGSDLSLKAYAIINGKELPFEEMNSKACDYMECPIKKGVQQDYVFN
VNVDMLKPRGKFNVRWLMKQGNENRCCFTNKFKIA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1223.t1 | Gene3D | G3DSA:2.60.40.770 | - | 23 | 155 | 9.6E-25 |
| 2 | g1223.t1 | PANTHER | PTHR11306 | NIEMANN PICK TYPE C2 PROTEIN NPC2-RELATED | 3 | 154 | 7.7E-22 |
| 3 | g1223.t1 | PANTHER | PTHR11306:SF55 | GEO08227P1-RELATED | 3 | 154 | 7.7E-22 |
| 1 | g1223.t1 | Pfam | PF02221 | ML domain | 26 | 153 | 1.3E-13 |
| 8 | g1223.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 9 | g1223.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 10 | g1223.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 15 | - |
| 11 | g1223.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 19 | - |
| 7 | g1223.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 155 | - |
| 14 | g1223.t1 | SMART | SM00737 | pgtp_13 | 26 | 152 | 5.2E-13 |
| 4 | g1223.t1 | SUPERFAMILY | SSF81296 | E set domains | 24 | 154 | 6.53E-25 |
| 5 | g1223.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 12 | g1223.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
| 13 | g1223.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 27 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K13443 (Niemann-Pick C2 protein)
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. There were no conditions that were differentially expressed