General information for g3740.t1
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.t1 | isoform | g3740.t1 | 27752247 | 27753077 |
| chr_3 | g3740 | g3740.t1 | exon | g3740.t1.exon1 | 27752247 | 27752422 |
| chr_3 | g3740 | g3740.t1 | cds | g3740.t1.CDS1 | 27752247 | 27752422 |
| chr_3 | g3740 | g3740.t1 | exon | g3740.t1.exon2 | 27752491 | 27752576 |
| chr_3 | g3740 | g3740.t1 | cds | g3740.t1.CDS2 | 27752491 | 27752576 |
| chr_3 | g3740 | g3740.t1 | exon | g3740.t1.exon3 | 27752656 | 27752884 |
| chr_3 | g3740 | g3740.t1 | cds | g3740.t1.CDS3 | 27752656 | 27752884 |
| chr_3 | g3740 | g3740.t1 | exon | g3740.t1.exon4 | 27752984 | 27753077 |
| chr_3 | g3740 | g3740.t1 | cds | g3740.t1.CDS4 | 27752984 | 27753077 |
| chr_3 | g3740 | g3740.t1 | TTS | g3740.t1 | 27753177 | 27753177 |
| chr_3 | g3740 | g3740.t1 | TSS | g3740.t1 | NA | NA |
Sequences
>g3740.t1 Gene=g3740 Length=585
ATGGCTGCAAAGTTTATGGGAGAACAGAAAATTGTTACAGGTTCACATGATCGTACACTT
AAGGTTTGGGATTTAAGAAGTAAAGCATGTTTTGAGACAAAATTTGCAGGTTCAAGTTGC
AATGATTTGGTTACAACTGATTTATCTACTGTTATAAGTGGACATTTTGATAAAAAAATT
CGTTTTTGGGACATACGCAGTCAAGATTCATCTTCAAGCATTGAAGTTTCTGCAAAAGTA
ACATCATTGGATCTATCGAAAGATTGCAAATTTCTTGCAACATGCATGCGTGATGATACT
ATAAAAATAATAGACTTGCGCACTAATCAAATTTTAACGACACTCTGCCACGATGGTTTC
AAAGTGGGATGCGACTTTTCCCGTATTTCATTAAATTCTGATAGTAGTTGCATAGCTGCC
GGATCTGCGGATGGCAGTGTCTTTATATGGAATATAGATGGGAAATTAATTTCAATTTTA
AAGGACCATAACGTTTCTGTACAGGCTGTGAGTTTCCATCCATTCAGCTCCGTATTGGCT
TCGGTAGACCGCGCAAAAAAATGCACTATATGGACTCATGGTTGA
>g3740.t1 Gene=g3740 Length=194
MAAKFMGEQKIVTGSHDRTLKVWDLRSKACFETKFAGSSCNDLVTTDLSTVISGHFDKKI
RFWDIRSQDSSSSIEVSAKVTSLDLSKDCKFLATCMRDDTIKIIDLRTNQILTTLCHDGF
KVGCDFSRISLNSDSSCIAAGSADGSVFIWNIDGKLISILKDHNVSVQAVSFHPFSSVLA
SVDRAKKCTIWTHG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g3740.t1 | Gene3D | G3DSA:2.130.10.10 | - | 6 | 81 | 1.1E-13 |
| 11 | g3740.t1 | Gene3D | G3DSA:2.130.10.10 | - | 82 | 193 | 4.4E-21 |
| 5 | g3740.t1 | PANTHER | PTHR19878:SF6 | AUTOPHAGY-RELATED PROTEIN 16-1 | 2 | 192 | 9.3E-59 |
| 6 | g3740.t1 | PANTHER | PTHR19878 | AUTOPHAGY PROTEIN 16-LIKE | 2 | 192 | 9.3E-59 |
| 8 | g3740.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 11 | 25 | 1.1E-7 |
| 7 | g3740.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 51 | 65 | 1.1E-7 |
| 9 | g3740.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 138 | 152 | 1.1E-7 |
| 4 | g3740.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 11 | 24 | 0.1 |
| 2 | g3740.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 41 | 64 | 0.057 |
| 1 | g3740.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 80 | 105 | 0.0064 |
| 3 | g3740.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 115 | 151 | 0.005 |
| 14 | g3740.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 11 | 25 | - |
| 13 | g3740.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 51 | 65 | - |
| 15 | g3740.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 138 | 152 | - |
| 20 | g3740.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 1 | 194 | 15.083 |
| 22 | g3740.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 11 | 33 | 10.542 |
| 23 | g3740.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 51 | 73 | 8.67 |
| 21 | g3740.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 129 | 153 | 8.871 |
| 17 | g3740.t1 | SMART | SM00320 | WD40_4 | 28 | 64 | 20.0 |
| 19 | g3740.t1 | SMART | SM00320 | WD40_4 | 67 | 105 | 0.38 |
| 18 | g3740.t1 | SMART | SM00320 | WD40_4 | 108 | 151 | 0.013 |
| 16 | g3740.t1 | SMART | SM00320 | WD40_4 | 153 | 192 | 0.0012 |
| 10 | g3740.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 9 | 191 | 5.72E-35 |
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 transcript has been annotated with K17890 (autophagy-related protein 16-1)
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.
