General information for g3738.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 g3738 is located on chr_3: 27738195..27739500 (+ 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 | g3738 | g3738.t1 | TSS | g3738.t1 | 27738116 | 27738116 |
| chr_3 | g3738 | g3738.t1 | isoform | g3738.t1 | 27738195 | 27739500 |
| chr_3 | g3738 | g3738.t1 | exon | g3738.t1.exon1 | 27738195 | 27738285 |
| chr_3 | g3738 | g3738.t1 | cds | g3738.t1.CDS1 | 27738195 | 27738285 |
| chr_3 | g3738 | g3738.t1 | exon | g3738.t1.exon2 | 27738345 | 27738615 |
| chr_3 | g3738 | g3738.t1 | cds | g3738.t1.CDS2 | 27738345 | 27738615 |
| chr_3 | g3738 | g3738.t1 | exon | g3738.t1.exon3 | 27738680 | 27738931 |
| chr_3 | g3738 | g3738.t1 | cds | g3738.t1.CDS3 | 27738680 | 27738931 |
| chr_3 | g3738 | g3738.t1 | exon | g3738.t1.exon4 | 27738996 | 27739267 |
| chr_3 | g3738 | g3738.t1 | cds | g3738.t1.CDS4 | 27738996 | 27739267 |
| chr_3 | g3738 | g3738.t1 | exon | g3738.t1.exon5 | 27739322 | 27739500 |
| chr_3 | g3738 | g3738.t1 | cds | g3738.t1.CDS5 | 27739322 | 27739500 |
| chr_3 | g3738 | g3738.t1 | TTS | g3738.t1 | NA | NA |
Sequences
>g3738.t1 Gene=g3738 Length=1065
ATGACAGAAAACGACTTCAGGAATATTATATTAAAGAGATTGACTGAAAGAAATGTACGA
GAGAGTAAATTTGAGGAAATGGTTTATTACACTCATCGTATGTTAGAGAGAAATTACGAG
TTGAAAAGCGAAAATTTAGCCATCACACTAGAAAATGAAAAACTTCGCAAAGGCATTGAT
GCGGGAGGAGGAATAGACTTGGGTTCAATCGCAAGAATACAATCACTCGAGAAGAAATTA
TTAGAGAAACAAGAAGAATTGATGGACCTTCATAAAAGAAAAAGTGACCATCAATCAATG
ATTATAGATTTAAATGTAAAAGTTAGTGATTTACAAAAACAGATTGAACATAAAAATATT
AGTCTAAATGAACAGCAAAAACTTAATCAAATGCTTAAAGCGGAAGTAAATCTACTAACA
GTCAAAGTTGGGAAACTTGAAGAATTAAATTCAACATTAAAAGATGAACACACGGCATTA
CATCTTCTTTTTGGCTCACTTGAGGAGAAACTAAAAAAAACGCAAGCAGAAAATGCTCAA
TTGTTAGAAAGATTAATGAAATCCAAAGCAAAAGATGCTGAAAAAATGAATGAAGAAAAT
GAGACATTTTTGAGAAAAAAGAATGACGCGATGAAACGAGAGCTTGCGGAAGCAATGGGC
AGTGATTCAAACACAATTCTTTCACCTCCCATCAATGAAGATGCCTTCTTTCACGGATGT
AGTGCGCCAAATGTATTTTTCGGAGATGAAATTCCAAACAAAGTTCATATGAAATTCGAC
TCTAATGATGGTGAAGTCAATGCTGTGAGATGGAGTCCGTTGATGGAAAGAATGATAGCC
ACTGGTGGTGCTGATAGAAAAGTTAAATTATGGGATGTAGGCAAAGGCAATACTTATGAA
TTAAGAGGAAATCTTATAGGAAGTAACCAAGCTGTTACAAGTCTCGATTTTGATTCAACA
GGAACACTAATATTAGCTTCATCCAATGATTATGCGAGTAGAGTTTGGGGTATTAACGAC
CACCGACTAAGAGTGAGTATAAATATAGTTATTCTTTCTATTTAA
>g3738.t1 Gene=g3738 Length=354
MTENDFRNIILKRLTERNVRESKFEEMVYYTHRMLERNYELKSENLAITLENEKLRKGID
AGGGIDLGSIARIQSLEKKLLEKQEELMDLHKRKSDHQSMIIDLNVKVSDLQKQIEHKNI
SLNEQQKLNQMLKAEVNLLTVKVGKLEELNSTLKDEHTALHLLFGSLEEKLKKTQAENAQ
LLERLMKSKAKDAEKMNEENETFLRKKNDAMKRELAEAMGSDSNTILSPPINEDAFFHGC
SAPNVFFGDEIPNKVHMKFDSNDGEVNAVRWSPLMERMIATGGADRKVKLWDVGKGNTYE
LRGNLIGSNQAVTSLDFDSTGTLILASSNDYASRVWGINDHRLRVSINIVILSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3738.t1 | Coils | Coil | Coil | 73 | 93 | - |
| 8 | g3738.t1 | Coils | Coil | Coil | 122 | 142 | - |
| 9 | g3738.t1 | Coils | Coil | Coil | 164 | 213 | - |
| 7 | g3738.t1 | Gene3D | G3DSA:2.130.10.10 | - | 91 | 349 | 3.7E-19 |
| 4 | g3738.t1 | PANTHER | PTHR19878:SF8 | AUTOPHAGY-RELATED 16, ISOFORM F | 2 | 346 | 9.2E-52 |
| 5 | g3738.t1 | PANTHER | PTHR19878 | AUTOPHAGY PROTEIN 16-LIKE | 2 | 346 | 9.2E-52 |
| 1 | g3738.t1 | Pfam | PF08614 | Autophagy protein 16 (ATG16) | 10 | 197 | 3.0E-33 |
| 3 | g3738.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 262 | 292 | 0.011 |
| 2 | g3738.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 301 | 336 | 0.031 |
| 11 | g3738.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 279 | 293 | - |
| 14 | g3738.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 259 | 346 | 18.273 |
| 15 | g3738.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 259 | 301 | 12.647 |
| 16 | g3738.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 305 | 346 | 10.676 |
| 13 | g3738.t1 | SMART | SM00320 | WD40_4 | 252 | 292 | 3.6E-7 |
| 12 | g3738.t1 | SMART | SM00320 | WD40_4 | 298 | 337 | 0.059 |
| 6 | g3738.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 232 | 344 | 6.0E-16 |
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.
