General information for g13384.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar protein sorting-associated protein 4A.
Parent gene
- The parent gene g13384 is located on chr_1: 29620442..29621850 (- 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 | g13384 | g13384.t1 | TTS | g13384.t1 | 29619487 | 29619487 |
| chr_1 | g13384 | g13384.t1 | isoform | g13384.t1 | 29619914 | 29621481 |
| chr_1 | g13384 | g13384.t1 | exon | g13384.t1.exon1 | 29619914 | 29620015 |
| chr_1 | g13384 | g13384.t1 | cds | g13384.t1.CDS1 | 29619914 | 29620015 |
| chr_1 | g13384 | g13384.t1 | exon | g13384.t1.exon2 | 29620075 | 29620785 |
| chr_1 | g13384 | g13384.t1 | cds | g13384.t1.CDS2 | 29620075 | 29620785 |
| chr_1 | g13384 | g13384.t1 | exon | g13384.t1.exon3 | 29620852 | 29621086 |
| chr_1 | g13384 | g13384.t1 | cds | g13384.t1.CDS3 | 29620852 | 29621086 |
| chr_1 | g13384 | g13384.t1 | exon | g13384.t1.exon4 | 29621146 | 29621284 |
| chr_1 | g13384 | g13384.t1 | cds | g13384.t1.CDS4 | 29621146 | 29621284 |
| chr_1 | g13384 | g13384.t1 | exon | g13384.t1.exon5 | 29621346 | 29621481 |
| chr_1 | g13384 | g13384.t1 | cds | g13384.t1.CDS5 | 29621346 | 29621481 |
| chr_1 | g13384 | g13384.t1 | TSS | g13384.t1 | 29621850 | 29621850 |
Sequences
>g13384.t1 Gene=g13384 Length=1323
ATGGCTGCTGGAACAACTTTACAAAAAGCTATTGATATAGTAACGAAAGCAACAGAGGAA
GATAGAAATAAAAATTATGAGGAAGCATTAAGGCTATATGAGCATGGTGTTGAATATTTT
CTTCACGCTATTAAATACGAAGCTCAAGGTGACAAAGCAAAAGAATCGATTAGAGCAAAA
TGTTTACAGTATCTTGATCGTGCAGAGAAACTCAAACAATATTTGAAAAAAGGAAAAAAG
CAGAAACCTGTAAAAGATGGAGATACAGGTTCCAAAGATAAAGATAAGAAAAGTGATAGT
GATTCAGATGAAGATGATCCAGAGAAAAAGAAACTTCAGAGTAAATTGGAAGGCGCAATT
GTTGTTGAGAAACCTAAGGTTAAATGGTCAGATGTAGCCGGTCTCGAAGGCGCTAAGGAA
GCGCTTAAAGAAGCAGTCATTCTGCCAATAAAATTTCCTCATTTATTTACTGGAAAAAGA
GTTCCATGGAAAGGAATTTTACTCTTTGGGCCACCAGGTACTGGTAAATCTTATTTGGCT
AAAGCTGTTGCAACAGAAGCAAATAATTCTACATTCTTCTCTGTATCGAGTGCTGATTTG
GTTTCAAAATGGCTCGGTGAATCAGAAAAGCTCGTTAGAAATCTCTTTGACTTGGCTCGT
GCTCACAAGCCTAGTATCATCTTTATCGATGAAGTTGACTCTTTATGTTCTTCTCGTTCT
GAAAACGAAAGTGAAAGTGCCCGTCGTATCAAAACCGAATTTCTTGTTCAAATGCAAGGT
GTAGGCAATGATAATGAAGGAATTCTCGTTCTTGGTGCGACAAATATTCCATGGGTTCTT
GATTCTGCTATTAGAAGACGTTTTGAAAAAAGAATTTATATACCTTTGCCTGAAGAAAAC
GCTCGCTTGGTCATGTTTAAAATTCATTTGGGCAACACATCGCATGTATTGACAGAAGAA
AATTTAAGACAACTCGCAAAACAAACTGAAGGTTATTCAGGTGCTGATATTTCAATTGTA
GTCCGTGATGCTCTTATGCAACCTGTTCGAAAAGTTCAGACAGCAACACATTTTAAAAGG
ATTCGCGGTCCATCGCCTTTGGATAAAAATGTAATGGTAGATGATCTTCTTACACCTTGC
TCGCCTGGTGAAAAAGGAGCAATTGAAATGACTTGGATGGAAGTTGAGGGAGAGAAACTT
TTTGAACCTCCAGTAACAATGGGTGACATGCTTAATTCACTTGCAAGAACAAAACCAACA
ATCAATGAAGACGATATGAAGAAACTGCAAAAGTTCACTGACGATTTTGGTCAGGAGGGT
TAA
>g13384.t1 Gene=g13384 Length=440
MAAGTTLQKAIDIVTKATEEDRNKNYEEALRLYEHGVEYFLHAIKYEAQGDKAKESIRAK
CLQYLDRAEKLKQYLKKGKKQKPVKDGDTGSKDKDKKSDSDSDEDDPEKKKLQSKLEGAI
VVEKPKVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRVPWKGILLFGPPGTGKSYLA
KAVATEANNSTFFSVSSADLVSKWLGESEKLVRNLFDLARAHKPSIIFIDEVDSLCSSRS
ENESESARRIKTEFLVQMQGVGNDNEGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEEN
ARLVMFKIHLGNTSHVLTEENLRQLAKQTEGYSGADISIVVRDALMQPVRKVQTATHFKR
IRGPSPLDKNVMVDDLLTPCSPGEKGAIEMTWMEVEGEKLFEPPVTMGDMLNSLARTKPT
INEDDMKKLQKFTDDFGQEG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g13384.t1 | CDD | cd02678 | MIT_VPS4 | 6 | 75 | 2.20082E-36 |
| 12 | g13384.t1 | CDD | cd00009 | AAA | 133 | 296 | 4.66902E-27 |
| 10 | g13384.t1 | Gene3D | G3DSA:1.20.58.280 | Hypothetical protein 1500032h18. | 2 | 86 | 6.2E-34 |
| 9 | g13384.t1 | Gene3D | G3DSA:3.40.50.300 | - | 125 | 429 | 1.1E-141 |
| 11 | g13384.t1 | Gene3D | G3DSA:1.10.8.60 | - | 298 | 420 | 1.1E-141 |
| 18 | g13384.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 112 | - |
| 17 | g13384.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 80 | 112 | - |
| 5 | g13384.t1 | PANTHER | PTHR23074:SF72 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4B | 6 | 438 | 1.6E-180 |
| 6 | g13384.t1 | PANTHER | PTHR23074 | AAA DOMAIN-CONTAINING | 6 | 438 | 1.6E-180 |
| 3 | g13384.t1 | Pfam | PF04212 | MIT (microtubule interacting and transport) domain | 7 | 73 | 3.6E-23 |
| 2 | g13384.t1 | Pfam | PF00004 | ATPase family associated with various cellular activities (AAA) | 166 | 296 | 6.4E-41 |
| 4 | g13384.t1 | Pfam | PF17862 | AAA+ lid domain | 321 | 354 | 4.6E-9 |
| 1 | g13384.t1 | Pfam | PF09336 | Vps4 C terminal oligomerisation domain | 377 | 437 | 2.2E-27 |
| 14 | g13384.t1 | ProSitePatterns | PS00674 | AAA-protein family signature. | 268 | 287 | - |
| 16 | g13384.t1 | SMART | SM00745 | smart | 3 | 82 | 2.5E-25 |
| 15 | g13384.t1 | SMART | SM00382 | AAA_5 | 162 | 298 | 2.9E-21 |
| 8 | g13384.t1 | SUPERFAMILY | SSF116846 | MIT domain | 5 | 85 | 1.14E-27 |
| 7 | g13384.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 125 | 434 | 5.49E-60 |
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:0005524 | ATP binding | MF |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K12196 (vacuolar protein-sorting-associated protein 4)
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.
