General information for g10404.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Gamma-aminobutyric acid receptor-associated protein.
Parent gene
- The parent gene g10404 is located on chr_1: 9570535..9571665 (- 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 | g10404 | g10404.t11 | isoform | g10404.t11 | 9569529 | 9571576 |
| chr_1 | g10404 | g10404.t11 | exon | g10404.t11.exon1 | 9569529 | 9570506 |
| chr_1 | g10404 | g10404.t11 | TTS | g10404.t11 | 9569533 | 9569533 |
| chr_1 | g10404 | g10404.t11 | cds | g10404.t11.CDS1 | 9570291 | 9570506 |
| chr_1 | g10404 | g10404.t11 | exon | g10404.t11.exon2 | 9571487 | 9571576 |
| chr_1 | g10404 | g10404.t11 | cds | g10404.t11.CDS2 | 9571487 | 9571576 |
| chr_1 | g10404 | g10404.t11 | TSS | g10404.t11 | 9571660 | 9571660 |
Sequences
>g10404.t11 Gene=g10404 Length=1068
ATGCATTTCCACTACAAAGAAGAACATCCATTTGAGAAGAGACGAGCTGAAGGTGATAAA
ATTCGTAAGAAGTATCCTGATAGAGTACCAAAAAAATATTTGGTACCATCGGACTTAACT
GTTGGACAATTTTATTTTCTAATTCGCAAACGTATTCATCTTCGTCCTGAGGACGCGCTT
TTCTTCTTTGTCAATAATGTAATTCCACCAACAAGTGCAACCATGGGCAGTCTCTATCAA
GAACATCATGAAGAAGATTTCTTCTTATACATTGCCTATTCTGACGAAAATGTCTATGGC
AATTAAATCAATGGACTTGAATCAAAGATAATGAATATTGTTACTCATATGAAGATGATG
AAAGTGGTTGAAATCTATAAATCAAGATTTCTTAAAAAAGAATCGCTATGCAGTGGAGTA
ACATATTAAATATATATTTAATAATTAACTTATGTGTGTGAAAAAAATCACTAGAAATTT
AAAAATTCAAAATGGATAAAAAAACGTTCGTGTAAGAAAATTCATTATCATTATTCTTCT
TCTTTAACTCAACACTACAGTTATGATTATATATTGAAAATACATAATTCACAATATATT
ACGCTAAAAAAAACTGTAACGTTAAAGTCCTCAAAAAAATTAACTTTAGTGTATATAAGA
TTTCATTTTGATTCTCTTTTCGTTTCTTCCCATACTTTATTTCCATTTAAACAAACAAAA
GAGAATGTACCTTAGAATTAATTATTTTAAAAATGTGATTGGAAACGATTGATGAGTTAG
TTTTCATAGCTACATGCTGTCAATATGAATTTTTGATAGCAATCGTTTCAACAAAAAAAT
TATAAAATAACGATTTAAAAATCCTAAAAATGATAAAAACGAATTAAAACCTTCAAAAAC
AGCAATTTGGTGAGTGGAATGGAATTATTTTTCTTTTAAAGCTGCACTTGAAAGTGTTTC
TCAATATAAAAAGATTTATTATTTCTATTCAAATTTTTATGTTTTATTTTAATGATTATT
GTAGTTGCTATAAATAAAGAAGGTTCTAATTTGGACCAATAAATAAAT
>g10404.t11 Gene=g10404 Length=101
MHFHYKEEHPFEKRRAEGDKIRKKYPDRVPKKYLVPSDLTVGQFYFLIRKRIHLRPEDAL
FFFVNNVIPPTSATMGSLYQEHHEEDFFLYIAYSDENVYGN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10404.t11 | Gene3D | G3DSA:3.10.20.90 | - | 1 | 101 | 0 |
| 2 | g10404.t11 | PANTHER | PTHR10969:SF33 | GABA(A) RECEPTOR-ASSOCIATED PROTEIN B | 1 | 30 | 0 |
| 4 | g10404.t11 | PANTHER | PTHR10969 | MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3-RELATED | 1 | 30 | 0 |
| 3 | g10404.t11 | PANTHER | PTHR10969:SF33 | GABA(A) RECEPTOR-ASSOCIATED PROTEIN B | 31 | 100 | 0 |
| 5 | g10404.t11 | PANTHER | PTHR10969 | MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3-RELATED | 31 | 100 | 0 |
| 1 | g10404.t11 | Pfam | PF02991 | Autophagy protein Atg8 ubiquitin like | 31 | 100 | 0 |
| 6 | g10404.t11 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 1 | 100 | 0 |
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 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.
