General information for g13172.t4
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.t4 | TSS | g13172.t4 | 28322010 | 28322010 |
| chr_1 | g13172 | g13172.t4 | isoform | g13172.t4 | 28322103 | 28323890 |
| chr_1 | g13172 | g13172.t4 | exon | g13172.t4.exon1 | 28322103 | 28322150 |
| chr_1 | g13172 | g13172.t4 | exon | g13172.t4.exon2 | 28322258 | 28323890 |
| chr_1 | g13172 | g13172.t4 | cds | g13172.t4.CDS1 | 28322874 | 28323890 |
| chr_1 | g13172 | g13172.t4 | TTS | g13172.t4 | 28324096 | 28324096 |
Sequences
>g13172.t4 Gene=g13172 Length=1681
ATGGATGCACAAGGAAGAAACGTTATAGTTTGCGATAATGGCACAGGTTTTGTAAAATGT
GGATATGCTGGAAGCAATTTCCCAGCACATATCTTTCCATCAATGGTTGGCAGGCCAACA
ATTCGAGCCGTAAATAAAATAGGAGATATTGAAGTAAAAGTGAGTTTTGAATCTATTGAG
CATCATTATTAATATTTTTCTTTTCTCTTTATCTGAATCTTATTTCTCTATAAAATATAT
TATATGATAGGATATTTTTCTCGGAGTAAGTCTTTTATAATGGAAAATAGTTGTGAATTT
TGTATTTTTCTTTCTTATTATTGTTGAATTGTTCACTTCATTCGTCATCCCGTTTTTTCG
TGTTATTTGCCTTTCTAGTTTTTATAAAACACTAACAAAATTTCATTACAATAATTCCTC
CTTTTTTACTTCCTTATTTATTGCTAAACTTAACATTTTTAATAAAAGGATGCCGGGTCT
TCGTTACCTGTAAGTAAAAATCTGTTCACTTTCTTCTCTTGTGTGACATTTGCATTGCAT
CCCCAGTGTTCTGTAGTTTCTAATTTAAATCATTCAAATTGCGTTGATGAATGTTTCTTT
TTTGGAATGACTAATGACATGATTTATATTCGAGGCTAATGTTTTATGCATTTTTTAGGA
TTTAATGGTAGGCGATGAAGCATCGCAATTACGATCAATGCTTGAAATTTCATATCCTAT
GGAAAACGGAATGGTTAGAAACTGGGAAGACATGTGTCACGTGTGGGATTATACATTTGG
TCCGAAAAAGATGAACATTGATCCTACAAATACAAAAATTCTATTGACTGAACCACCACT
GAATCCATTAAAAAATCGTGAAAAGATGATTGAAGTGATGTTTGAAAAATATGGTTTTCA
TTCAACTTATATTGCAATTCAAGCTGTACTGACTCTTTACGCACAAGGTCTCATTTCGGG
CGTTGTCATCGATTCAGGCGATGGTGTAACACATATTTGCCCAGTTTATGAATCATATGC
ACTGCCACATTTAACAAAAAGATTGGATATTGCTGGTCGTGATATTACAAAGTATCTTAT
TAAGCTATTGCTCCTTCGTGGCTATGCATTCAATCATTCTGCTGATTTCGAGACTGTTCG
TATGATGAAAGAAAAATTGTGTTATATCGGTTATGATATTGAAATGGAACAAAAGTTGGC
ATTAGAAACGACTGTTCTTGTTGAATCATATACATTGCCAGATGGTCGTGTCATTAAAGT
TGGTGGTGAGCGATTTGAAGCTCCTGAAGCACTTTTCCAGCCTCACTTGATAAATGTTGA
AGGACAGGGAATTGCTGAATTAGTTTTTAATACAATTCAAGCTGCCGATATAGACATGCG
TCCGGAACTTTATAAAAGAATTGTATTATCGGGTGGGTCTACAATGTATCCGGGTCTTCC
CTCTCGTCTTGAACGCGAAATTAAGCAATTATACCTTGAGAGAGTGTTAAAAAATGACAT
TGATAAACTTTCGAAATTCAAAATTCGAATTGATGACCCACCAAGACGAAAGGATATGGT
TTTTATTGGAGGAGCAGTTCTTGCTGGTTTAAATAAGAACAAAGATGAATTCTGGATGTC
AAAGCAAGAGTATCAAGAAATGGGCTTGAAAGTTCTCTCTAAATGGGGAGCAAGAGCATA
A
>g13172.t4 Gene=g13172 Length=338
MVGDEASQLRSMLEISYPMENGMVRNWEDMCHVWDYTFGPKKMNIDPTNTKILLTEPPLN
PLKNREKMIEVMFEKYGFHSTYIAIQAVLTLYAQGLISGVVIDSGDGVTHICPVYESYAL
PHLTKRLDIAGRDITKYLIKLLLLRGYAFNHSADFETVRMMKEKLCYIGYDIEMEQKLAL
ETTVLVESYTLPDGRVIKVGGERFEAPEALFQPHLINVEGQGIAELVFNTIQAADIDMRP
ELYKRIVLSGGSTMYPGLPSRLEREIKQLYLERVLKNDIDKLSKFKIRIDDPPRRKDMVF
IGGAVLAGLNKNKDEFWMSKQEYQEMGLKVLSKWGARA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g13172.t4 | CDD | cd00012 | NBD_sugar-kinase_HSP70_actin | 16 | 130 | 2.01264E-13 |
| 11 | g13172.t4 | Gene3D | G3DSA:3.30.420.40 | - | 1 | 327 | 2.9E-131 |
| 12 | g13172.t4 | Gene3D | G3DSA:3.30.420.40 | - | 86 | 304 | 2.9E-131 |
| 10 | g13172.t4 | Gene3D | G3DSA:3.90.640.10 | Actin; Chain A | 130 | 218 | 2.9E-131 |
| 2 | g13172.t4 | PANTHER | PTHR11937:SF409 | ACTIN-RELATED PROTEIN 2 | 1 | 334 | 2.3E-191 |
| 3 | g13172.t4 | PANTHER | PTHR11937 | ACTIN | 1 | 334 | 2.3E-191 |
| 6 | g13172.t4 | PRINTS | PR00190 | Actin signature | 9 | 31 | 4.6E-24 |
| 5 | g13172.t4 | PRINTS | PR00190 | Actin signature | 64 | 77 | 4.6E-24 |
| 7 | g13172.t4 | PRINTS | PR00190 | Actin signature | 89 | 108 | 4.6E-24 |
| 4 | g13172.t4 | PRINTS | PR00190 | Actin signature | 185 | 201 | 4.6E-24 |
| 1 | g13172.t4 | Pfam | PF00022 | Actin | 2 | 332 | 5.4E-91 |
| 14 | g13172.t4 | ProSitePatterns | PS01132 | Actins and actin-related proteins signature. | 53 | 65 | - |
| 15 | g13172.t4 | SMART | SM00268 | actin_3 | 1 | 335 | 1.5E-143 |
| 9 | g13172.t4 | SUPERFAMILY | SSF53067 | Actin-like ATPase domain | 2 | 102 | 1.07E-33 |
| 8 | g13172.t4 | SUPERFAMILY | SSF53067 | Actin-like ATPase domain | 95 | 332 | 1.02E-72 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
