General information for g8948.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Semaphorin-2A.
Parent gene
- The parent gene g8948 is located on chr_2: 34070792..34107159 (+ 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 | g8948 | g8948.t3 | TSS | g8948.t3 | 34069169 | 34069169 |
| chr_2 | g8948 | g8948.t3 | isoform | g8948.t3 | 34069347 | 34082520 |
| chr_2 | g8948 | g8948.t3 | exon | g8948.t3.exon1 | 34069347 | 34069559 |
| chr_2 | g8948 | g8948.t3 | TTS | g8948.t3 | 34069453 | 34069453 |
| chr_2 | g8948 | g8948.t3 | exon | g8948.t3.exon2 | 34070512 | 34070963 |
| chr_2 | g8948 | g8948.t3 | cds | g8948.t3.CDS1 | 34070792 | 34070963 |
| chr_2 | g8948 | g8948.t3 | exon | g8948.t3.exon3 | 34078725 | 34078812 |
| chr_2 | g8948 | g8948.t3 | cds | g8948.t3.CDS2 | 34078725 | 34078812 |
| chr_2 | g8948 | g8948.t3 | exon | g8948.t3.exon4 | 34082200 | 34082251 |
| chr_2 | g8948 | g8948.t3 | cds | g8948.t3.CDS3 | 34082200 | 34082251 |
| chr_2 | g8948 | g8948.t3 | exon | g8948.t3.exon5 | 34082357 | 34082520 |
| chr_2 | g8948 | g8948.t3 | cds | g8948.t3.CDS4 | 34082357 | 34082371 |
Sequences
>g8948.t3 Gene=g8948 Length=969
AACATTTTTAAATAAATTTTTTTAAGTTGTTTCTTTTTTTATTTTTATGATTTCCAACAC
ATAAGTTGCTCAACTGTAAAAAATATATAAAATTAAATGTAAAAAAAAAATACACAAGTG
AAAAGAGAAAGAGAGAGAATTGTTACATGTGAAGAAGTGGAATGAAAGAATGGTAGAAAA
AAAAATGTCTGAATTATTATAGTGTGAATAAAGGCTTTTTTGATGACACCGAAATGAGAA
AATAATATCTGTTCAGTCTCAGTCAGTTAGTGAAGAAGAAATACGAAATGTTAATAATAA
TTGAATGAAGAAGGAAAGAAGGAAAAGTGAAAAGAAGAACAGATAATAAAATTCTGTATA
TGTTGTATATTTTTATATTCTTTCGCCTTGTGTGAAGTTCATATTATCGAATTAGGCGCT
AAAGAAGAAAAAGTGAAGAAGATATAAAGCAAAGAGGACGATATAATAACATAATAATAA
TAACGAGCCGAAAATGAAGTTGAATAAGTTGAAAATGTCTTATTTATCGAGTAGTGTCAG
TGTGTTGTTCATTTTCTTATTTCTATTGGATAATACGATCGTTCTTGCCGATTATGAAAA
TACATTTAGTAGTTATTTTGAGCAGCAATGCTGTAATGGACCACATCATCTAAGGCATCA
TAAAGATCATGTACGAGAATTCACATGTGGAAAGTTATACTATAGAACATTCCATTTAGA
TGAAGACAGAGATGCGCTTTATGTTGGTGCTATGGATAGAGTGTATAAATTAAACCTTAA
AAATATCACACTAACAGGATGCGAGTGGAAAATTCTGTAGCTCATAAAAGGGACAATTTG
GGAATTAGTGAAAATAAATCGATTGATAATTATTGATTGGTTATTGAATGGAATTAAAAC
GCAATGTGATGTGTATGCATCATCAAAGAAAAGCTTAACATTAAATTGAATAAAACTATT
GGAATTAAA
>g8948.t3 Gene=g8948 Length=108
MKLNKLKMSYLSSSVSVLFIFLFLLDNTIVLADYENTFSSYFEQQCCNGPHHLRHHKDHV
REFTCGKLYYRTFHLDEDRDALYVGAMDRVYKLNLKNITLTGCEWKIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8948.t3 | Gene3D | G3DSA:2.130.10.10 | - | 33 | 107 | 5.9E-7 |
| 2 | g8948.t3 | PANTHER | PTHR11036:SF90 | SEMAPHORIN 2B, ISOFORM D-RELATED | 13 | 106 | 1.0E-21 |
| 3 | g8948.t3 | PANTHER | PTHR11036 | SEMAPHORIN | 13 | 106 | 1.0E-21 |
| 1 | g8948.t3 | Pfam | PF01403 | Sema domain | 72 | 101 | 1.8E-6 |
| 9 | g8948.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 32 | - |
| 10 | g8948.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 13 | - |
| 11 | g8948.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 14 | 25 | - |
| 12 | g8948.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 26 | 32 | - |
| 8 | g8948.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 33 | 108 | - |
| 4 | g8948.t3 | SUPERFAMILY | SSF101912 | Sema domain | 60 | 102 | 8.89E-10 |
| 6 | g8948.t3 | SignalP_EUK | SignalP-TM | SignalP-TM | 1 | 32 | - |
| 5 | g8948.t3 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 32 | - |
| 13 | g8948.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 10 | 32 | - |
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:0030215 | semaphorin receptor binding | MF |
| GO:0005515 | protein binding | MF |
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