General information for g3740.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Autophagy-related protein 16-1.
Parent gene
- The parent gene g3740 is located on chr_3: 27752247..27753077 (+ 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 | g3740 | g3740.t2 | isoform | g3740.t2 | 27752247 | 27753077 |
| chr_3 | g3740 | g3740.t2 | exon | g3740.t2.exon1 | 27752247 | 27752422 |
| chr_3 | g3740 | g3740.t2 | cds | g3740.t2.CDS1 | 27752247 | 27752422 |
| chr_3 | g3740 | g3740.t2 | exon | g3740.t2.exon2 | 27752491 | 27752580 |
| chr_3 | g3740 | g3740.t2 | cds | g3740.t2.CDS2 | 27752491 | 27752580 |
| chr_3 | g3740 | g3740.t2 | exon | g3740.t2.exon3 | 27752656 | 27752884 |
| chr_3 | g3740 | g3740.t2 | cds | g3740.t2.CDS3 | 27752656 | 27752686 |
| chr_3 | g3740 | g3740.t2 | exon | g3740.t2.exon4 | 27752984 | 27753077 |
| chr_3 | g3740 | g3740.t2 | TTS | g3740.t2 | 27753177 | 27753177 |
| chr_3 | g3740 | g3740.t2 | TSS | g3740.t2 | NA | NA |
Sequences
>g3740.t2 Gene=g3740 Length=589
ATGGCTGCAAAGTTTATGGGAGAACAGAAAATTGTTACAGGTTCACATGATCGTACACTT
AAGGTTTGGGATTTAAGAAGTAAAGCATGTTTTGAGACAAAATTTGCAGGTTCAAGTTGC
AATGATTTGGTTACAACTGATTTATCTACTGTTATAAGTGGACATTTTGATAAAAAAATT
CGTTTTTGGGACATACGCAGTCAAGATTCATCTTCAAGCATTGAAGTTTCTGCAAAAGTA
ACATCATTGGATCTATCGAAAGGCAAATTGCAAATTTCTTGCAACATGCATGCGTGATGA
TACTATAAAAATAATAGACTTGCGCACTAATCAAATTTTAACGACACTCTGCCACGATGG
TTTCAAAGTGGGATGCGACTTTTCCCGTATTTCATTAAATTCTGATAGTAGTTGCATAGC
TGCCGGATCTGCGGATGGCAGTGTCTTTATATGGAATATAGATGGGAAATTAATTTCAAT
TTTAAAGGACCATAACGTTTCTGTACAGGCTGTGAGTTTCCATCCATTCAGCTCCGTATT
GGCTTCGGTAGACCGCGCAAAAAAATGCACTATATGGACTCATGGTTGA
>g3740.t2 Gene=g3740 Length=98
MAAKFMGEQKIVTGSHDRTLKVWDLRSKACFETKFAGSSCNDLVTTDLSTVISGHFDKKI
RFWDIRSQDSSSSIEVSAKVTSLDLSKGKLQISCNMHA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3740.t2 | Gene3D | G3DSA:2.130.10.10 | - | 6 | 97 | 2.3E-16 |
| 3 | g3740.t2 | PANTHER | PTHR19878:SF6 | AUTOPHAGY-RELATED PROTEIN 16-1 | 2 | 92 | 6.5E-30 |
| 4 | g3740.t2 | PANTHER | PTHR19878 | AUTOPHAGY PROTEIN 16-LIKE | 2 | 92 | 6.5E-30 |
| 2 | g3740.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 11 | 24 | 0.038 |
| 1 | g3740.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 37 | 64 | 0.017 |
| 7 | g3740.t2 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 11 | 25 | - |
| 6 | g3740.t2 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 51 | 65 | - |
| 9 | g3740.t2 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 1 | 73 | 11.946 |
| 10 | g3740.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 11 | 33 | 10.542 |
| 11 | g3740.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 51 | 73 | 8.67 |
| 5 | g3740.t2 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 5 | 96 | 1.03E-15 |
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