General information for g10404.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t5 | isoform | g10404.t5 | 9564713 | 9571576 |
| chr_1 | g10404 | g10404.t5 | exon | g10404.t5.exon1 | 9564713 | 9564722 |
| chr_1 | g10404 | g10404.t5 | exon | g10404.t5.exon2 | 9569549 | 9570554 |
| chr_1 | g10404 | g10404.t5 | cds | g10404.t5.CDS1 | 9570291 | 9570554 |
| chr_1 | g10404 | g10404.t5 | exon | g10404.t5.exon3 | 9571487 | 9571576 |
| chr_1 | g10404 | g10404.t5 | cds | g10404.t5.CDS2 | 9571487 | 9571576 |
| chr_1 | g10404 | g10404.t5 | TSS | g10404.t5 | 9571660 | 9571660 |
| chr_1 | g10404 | g10404.t5 | TTS | g10404.t5 | NA | NA |
Sequences
>g10404.t5 Gene=g10404 Length=1106
ATGCATTTCCACTACAAAGAAGAACATCCATTTGAGAAGAGACGAGCTGAAGGTGATAAA
ATTCGTAAGAAGTATCCTGATAGAGTACCAGTCATCGTTGAAAAGGCACCAAAAGCAAGA
ATCGGTGATCTTGATAAGAAAAAATATTTGGTACCATCGGACTTAACTGTTGGACAATTT
TATTTTCTAATTCGCAAACGTATTCATCTTCGTCCTGAGGACGCGCTTTTCTTCTTTGTC
AATAATGTAATTCCACCAACAAGTGCAACCATGGGCAGTCTCTATCAAGAACATCATGAA
GAAGATTTCTTCTTATACATTGCCTATTCTGACGAAAATGTCTATGGCAATTAAATCAAT
GGACTTGAATCAAAGATAATGAATATTGTTACTCATATGAAGATGATGAAAGTGGTTGAA
ATCTATAAATCAAGATTTCTTAAAAAAGAATCGCTATGCAGTGGAGTAACATATTAAATA
TATATTTAATAATTAACTTATGTGTGTGAAAAAAATCACTAGAAATTTAAAAATTCAAAA
TGGATAAAAAAACGTTCGTGTAAGAAAATTCATTATCATTATTCTTCTTCTTTAACTCAA
CACTACAGTTATGATTATATATTGAAAATACATAATTCACAATATATTACGCTAAAAAAA
ACTGTAACGTTAAAGTCCTCAAAAAAATTAACTTTAGTGTATATAAGATTTCATTTTGAT
TCTCTTTTCGTTTCTTCCCATACTTTATTTCCATTTAAACAAACAAAAGAGAATGTACCT
TAGAATTAATTATTTTAAAAATGTGATTGGAAACGATTGATGAGTTAGTTTTCATAGCTA
CATGCTGTCAATATGAATTTTTGATAGCAATCGTTTCAACAAAAAAATTATAAAATAACG
ATTTAAAAATCCTAAAAATGATAAAAACGAATTAAAACCTTCAAAAACAGCAATTTGGTG
AGTGGAATGGAATTATTTTTCTTTTAAAGCTGCACTTGAAAGTGTTTCTCAATATAAAAA
GATTTATTATTTCTATTCAAATTTTTATGTTTTATTTTAATGATTATTGTAGTTGCTATA
AATAAAGAAGGTTCTAGAAAAAAATT
>g10404.t5 Gene=g10404 Length=117
MHFHYKEEHPFEKRRAEGDKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQF
YFLIRKRIHLRPEDALFFFVNNVIPPTSATMGSLYQEHHEEDFFLYIAYSDENVYGN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10404.t5 | CDD | cd17232 | Ubl_ATG8_GABARAP | 3 | 116 | 0 |
| 5 | g10404.t5 | Gene3D | G3DSA:3.10.20.90 | - | 1 | 117 | 0 |
| 2 | g10404.t5 | PANTHER | PTHR10969:SF55 | GABA(A) RECEPTOR ASSOCIATED PROTEIN | 1 | 116 | 0 |
| 3 | g10404.t5 | PANTHER | PTHR10969 | MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3-RELATED | 1 | 116 | 0 |
| 1 | g10404.t5 | Pfam | PF02991 | Autophagy protein Atg8 ubiquitin like | 13 | 116 | 0 |
| 4 | g10404.t5 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 1 | 116 | 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 transcript has been annotated with K08341 (GABA(A) receptor-associated 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.
