General information for g13172.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Actin-related protein 2.
Parent gene
- The parent gene g13172 is located on chr_1: 28322868..28324101 (+ 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 | g13172 | g13172.t1 | TSS | g13172.t1 | 28322010 | 28322010 |
| chr_1 | g13172 | g13172.t1 | isoform | g13172.t1 | 28322103 | 28323890 |
| chr_1 | g13172 | g13172.t1 | exon | g13172.t1.exon1 | 28322103 | 28322150 |
| chr_1 | g13172 | g13172.t1 | cds | g13172.t1.CDS1 | 28322103 | 28322150 |
| chr_1 | g13172 | g13172.t1 | exon | g13172.t1.exon2 | 28322258 | 28322368 |
| chr_1 | g13172 | g13172.t1 | cds | g13172.t1.CDS2 | 28322258 | 28322368 |
| chr_1 | g13172 | g13172.t1 | exon | g13172.t1.exon3 | 28322868 | 28323890 |
| chr_1 | g13172 | g13172.t1 | cds | g13172.t1.CDS3 | 28322868 | 28323890 |
| chr_1 | g13172 | g13172.t1 | TTS | g13172.t1 | 28324096 | 28324096 |
Sequences
>g13172.t1 Gene=g13172 Length=1182
ATGGATGCACAAGGAAGAAACGTTATAGTTTGCGATAATGGCACAGGTTTTGTAAAATGT
GGATATGCTGGAAGCAATTTCCCAGCACATATCTTTCCATCAATGGTTGGCAGGCCAACA
ATTCGAGCCGTAAATAAAATAGGAGATATTGAAGTAAAAGATTTAATGGTAGGCGATGAA
GCATCGCAATTACGATCAATGCTTGAAATTTCATATCCTATGGAAAACGGAATGGTTAGA
AACTGGGAAGACATGTGTCACGTGTGGGATTATACATTTGGTCCGAAAAAGATGAACATT
GATCCTACAAATACAAAAATTCTATTGACTGAACCACCACTGAATCCATTAAAAAATCGT
GAAAAGATGATTGAAGTGATGTTTGAAAAATATGGTTTTCATTCAACTTATATTGCAATT
CAAGCTGTACTGACTCTTTACGCACAAGGTCTCATTTCGGGCGTTGTCATCGATTCAGGC
GATGGTGTAACACATATTTGCCCAGTTTATGAATCATATGCACTGCCACATTTAACAAAA
AGATTGGATATTGCTGGTCGTGATATTACAAAGTATCTTATTAAGCTATTGCTCCTTCGT
GGCTATGCATTCAATCATTCTGCTGATTTCGAGACTGTTCGTATGATGAAAGAAAAATTG
TGTTATATCGGTTATGATATTGAAATGGAACAAAAGTTGGCATTAGAAACGACTGTTCTT
GTTGAATCATATACATTGCCAGATGGTCGTGTCATTAAAGTTGGTGGTGAGCGATTTGAA
GCTCCTGAAGCACTTTTCCAGCCTCACTTGATAAATGTTGAAGGACAGGGAATTGCTGAA
TTAGTTTTTAATACAATTCAAGCTGCCGATATAGACATGCGTCCGGAACTTTATAAAAGA
ATTGTATTATCGGGTGGGTCTACAATGTATCCGGGTCTTCCCTCTCGTCTTGAACGCGAA
ATTAAGCAATTATACCTTGAGAGAGTGTTAAAAAATGACATTGATAAACTTTCGAAATTC
AAAATTCGAATTGATGACCCACCAAGACGAAAGGATATGGTTTTTATTGGAGGAGCAGTT
CTTGCTGGTTTAAATAAGAACAAAGATGAATTCTGGATGTCAAAGCAAGAGTATCAAGAA
ATGGGCTTGAAAGTTCTCTCTAAATGGGGAGCAAGAGCATAA
>g13172.t1 Gene=g13172 Length=393
MDAQGRNVIVCDNGTGFVKCGYAGSNFPAHIFPSMVGRPTIRAVNKIGDIEVKDLMVGDE
ASQLRSMLEISYPMENGMVRNWEDMCHVWDYTFGPKKMNIDPTNTKILLTEPPLNPLKNR
EKMIEVMFEKYGFHSTYIAIQAVLTLYAQGLISGVVIDSGDGVTHICPVYESYALPHLTK
RLDIAGRDITKYLIKLLLLRGYAFNHSADFETVRMMKEKLCYIGYDIEMEQKLALETTVL
VESYTLPDGRVIKVGGERFEAPEALFQPHLINVEGQGIAELVFNTIQAADIDMRPELYKR
IVLSGGSTMYPGLPSRLEREIKQLYLERVLKNDIDKLSKFKIRIDDPPRRKDMVFIGGAV
LAGLNKNKDEFWMSKQEYQEMGLKVLSKWGARA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g13172.t1 | CDD | cd00012 | NBD_sugar-kinase_HSP70_actin | 9 | 185 | 5.14417E-13 |
| 13 | g13172.t1 | Gene3D | G3DSA:3.30.420.40 | - | 9 | 382 | 5.5E-148 |
| 14 | g13172.t1 | Gene3D | G3DSA:3.30.420.40 | - | 141 | 359 | 5.5E-148 |
| 12 | g13172.t1 | Gene3D | G3DSA:3.90.640.10 | Actin; Chain A | 185 | 273 | 5.5E-148 |
| 2 | g13172.t1 | PANTHER | PTHR11937:SF149 | ACTIN-RELATED PROTEIN 2-A-RELATED | 1 | 389 | 5.5E-220 |
| 3 | g13172.t1 | PANTHER | PTHR11937 | ACTIN | 1 | 389 | 5.5E-220 |
| 6 | g13172.t1 | PRINTS | PR00190 | Actin signature | 27 | 36 | 1.3E-29 |
| 5 | g13172.t1 | PRINTS | PR00190 | Actin signature | 52 | 63 | 1.3E-29 |
| 8 | g13172.t1 | PRINTS | PR00190 | Actin signature | 64 | 86 | 1.3E-29 |
| 4 | g13172.t1 | PRINTS | PR00190 | Actin signature | 119 | 132 | 1.3E-29 |
| 7 | g13172.t1 | PRINTS | PR00190 | Actin signature | 144 | 163 | 1.3E-29 |
| 9 | g13172.t1 | PRINTS | PR00190 | Actin signature | 240 | 256 | 1.3E-29 |
| 1 | g13172.t1 | Pfam | PF00022 | Actin | 7 | 387 | 3.7E-103 |
| 16 | g13172.t1 | ProSitePatterns | PS01132 | Actins and actin-related proteins signature. | 108 | 120 | - |
| 17 | g13172.t1 | SMART | SM00268 | actin_3 | 6 | 390 | 7.8E-184 |
| 11 | g13172.t1 | SUPERFAMILY | SSF53067 | Actin-like ATPase domain | 6 | 157 | 5.76E-52 |
| 10 | g13172.t1 | SUPERFAMILY | SSF53067 | Actin-like ATPase domain | 150 | 387 | 1.57E-72 |
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:0005856 | cytoskeleton | CC |
| GO:0007015 | actin filament organization | BP |
| GO:0005885 | Arp2/3 protein complex | CC |
| GO:0034314 | Arp2/3 complex-mediated actin nucleation | BP |
| GO:0005524 | ATP binding | MF |
KEGG
Orthology
- This transcript has been annotated with K17260 (actin-related protein 2)
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.
