General information for g12811.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Netrin-A.
Parent gene
- The parent gene g12811 is located on chr_1: 26361750..26362170 (- 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_1 | g12811 | g12811.t1 | isoform | g12811.t1 | 26361750 | 26362170 |
| chr_1 | g12811 | g12811.t1 | exon | g12811.t1.exon1 | 26361750 | 26361885 |
| chr_1 | g12811 | g12811.t1 | cds | g12811.t1.CDS1 | 26361750 | 26361885 |
| chr_1 | g12811 | g12811.t1 | exon | g12811.t1.exon2 | 26361953 | 26362170 |
| chr_1 | g12811 | g12811.t1 | cds | g12811.t1.CDS2 | 26361953 | 26362170 |
| chr_1 | g12811 | g12811.t1 | TSS | g12811.t1 | NA | NA |
| chr_1 | g12811 | g12811.t1 | TTS | g12811.t1 | NA | NA |
Sequences
>g12811.t1 Gene=g12811 Length=354
ATGGCAAAAGTTATTGCACGAGAGGCTGTAGCGACGACAACGAAATCCAACGAGGATCAA
AGCAAGTCAGAATCTGTAAAATTCACACTTCAAGTGAAGGCAATTTTCCGCAAGACAGAC
GACAGTGTGGTGAGCAATTTACCAAAGAAACAAAATATTTCTATGTATGTTTTCACCAGA
GATCTTGACTGCAAATGTCCCAAGATCAAAGTCAAAAAATCTTATCTCATTCTTGGAAGT
GATGATGAAGGTCCAGCAAATGCCCTCGGCATTGGTGAAAACTCAATTGTCATCGAATGG
CGTGATGAATGGTATAGACGCCTACGAAAATATCAACGGCAGACGTGTGATTAA
>g12811.t1 Gene=g12811 Length=117
MAKVIAREAVATTTKSNEDQSKSESVKFTLQVKAIFRKTDDSVVSNLPKKQNISMYVFTR
DLDCKCPKIKVKKSYLILGSDDEGPANALGIGENSIVIEWRDEWYRRLRKYQRQTCD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g12811.t1 | Gene3D | G3DSA:2.40.50.120 | - | 5 | 117 | 0.000 |
| 1 | g12811.t1 | Pfam | PF01759 | UNC-6/NTR/C345C module | 17 | 113 | 0.000 |
| 5 | g12811.t1 | ProSiteProfiles | PS50189 | NTR domain profile. | 1 | 116 | 15.492 |
| 3 | g12811.t1 | SMART | SM00643 | c345c | 1 | 114 | 0.000 |
| 2 | g12811.t1 | SUPERFAMILY | SSF50242 | TIMP-like | 22 | 117 | 0.000 |
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: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