Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin-related protein 2.

Parent gene

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.t3 TSS g13172.t3 28322010 28322010
chr_1 g13172 g13172.t3 isoform g13172.t3 28322103 28323890
chr_1 g13172 g13172.t3 exon g13172.t3.exon1 28322103 28322148
chr_1 g13172 g13172.t3 cds g13172.t3.CDS1 28322140 28322148
chr_1 g13172 g13172.t3 exon g13172.t3.exon2 28322258 28322368
chr_1 g13172 g13172.t3 cds g13172.t3.CDS2 28322258 28322368
chr_1 g13172 g13172.t3 exon g13172.t3.exon3 28322868 28323890
chr_1 g13172 g13172.t3 cds g13172.t3.CDS3 28322868 28323890
chr_1 g13172 g13172.t3 TTS g13172.t3 28324096 28324096

Sequences

>g13172.t3 Gene=g13172 Length=1180
ATGGATGCACAAGGAAGAAACGTTATAGTTTGCGATAATGGCACAGTTTGTAAAATGTGG
ATATGCTGGAAGCAATTTCCCAGCACATATCTTTCCATCAATGGTTGGCAGGCCAACAAT
TCGAGCCGTAAATAAAATAGGAGATATTGAAGTAAAAGATTTAATGGTAGGCGATGAAGC
ATCGCAATTACGATCAATGCTTGAAATTTCATATCCTATGGAAAACGGAATGGTTAGAAA
CTGGGAAGACATGTGTCACGTGTGGGATTATACATTTGGTCCGAAAAAGATGAACATTGA
TCCTACAAATACAAAAATTCTATTGACTGAACCACCACTGAATCCATTAAAAAATCGTGA
AAAGATGATTGAAGTGATGTTTGAAAAATATGGTTTTCATTCAACTTATATTGCAATTCA
AGCTGTACTGACTCTTTACGCACAAGGTCTCATTTCGGGCGTTGTCATCGATTCAGGCGA
TGGTGTAACACATATTTGCCCAGTTTATGAATCATATGCACTGCCACATTTAACAAAAAG
ATTGGATATTGCTGGTCGTGATATTACAAAGTATCTTATTAAGCTATTGCTCCTTCGTGG
CTATGCATTCAATCATTCTGCTGATTTCGAGACTGTTCGTATGATGAAAGAAAAATTGTG
TTATATCGGTTATGATATTGAAATGGAACAAAAGTTGGCATTAGAAACGACTGTTCTTGT
TGAATCATATACATTGCCAGATGGTCGTGTCATTAAAGTTGGTGGTGAGCGATTTGAAGC
TCCTGAAGCACTTTTCCAGCCTCACTTGATAAATGTTGAAGGACAGGGAATTGCTGAATT
AGTTTTTAATACAATTCAAGCTGCCGATATAGACATGCGTCCGGAACTTTATAAAAGAAT
TGTATTATCGGGTGGGTCTACAATGTATCCGGGTCTTCCCTCTCGTCTTGAACGCGAAAT
TAAGCAATTATACCTTGAGAGAGTGTTAAAAAATGACATTGATAAACTTTCGAAATTCAA
AATTCGAATTGATGACCCACCAAGACGAAAGGATATGGTTTTTATTGGAGGAGCAGTTCT
TGCTGGTTTAAATAAGAACAAAGATGAATTCTGGATGTCAAAGCAAGAGTATCAAGAAAT
GGGCTTGAAAGTTCTCTCTAAATGGGGAGCAAGAGCATAA

>g13172.t3 Gene=g13172 Length=380
MAQFVKCGYAGSNFPAHIFPSMVGRPTIRAVNKIGDIEVKDLMVGDEASQLRSMLEISYP
MENGMVRNWEDMCHVWDYTFGPKKMNIDPTNTKILLTEPPLNPLKNREKMIEVMFEKYGF
HSTYIAIQAVLTLYAQGLISGVVIDSGDGVTHICPVYESYALPHLTKRLDIAGRDITKYL
IKLLLLRGYAFNHSADFETVRMMKEKLCYIGYDIEMEQKLALETTVLVESYTLPDGRVIK
VGGERFEAPEALFQPHLINVEGQGIAELVFNTIQAADIDMRPELYKRIVLSGGSTMYPGL
PSRLEREIKQLYLERVLKNDIDKLSKFKIRIDDPPRRKDMVFIGGAVLAGLNKNKDEFWM
SKQEYQEMGLKVLSKWGARA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g13172.t3 CDD cd00012 NBD_sugar-kinase_HSP70_actin 58 172 4.07239E-13
14 g13172.t3 Gene3D G3DSA:3.30.420.40 - 3 369 9.2E-143
13 g13172.t3 Gene3D G3DSA:3.30.420.40 - 128 346 9.2E-143
12 g13172.t3 Gene3D G3DSA:3.90.640.10 Actin; Chain A 172 260 9.2E-143
2 g13172.t3 PANTHER PTHR11937:SF149 ACTIN-RELATED PROTEIN 2-A-RELATED 3 376 1.8E-209
3 g13172.t3 PANTHER PTHR11937 ACTIN 3 376 1.8E-209
9 g13172.t3 PRINTS PR00190 Actin signature 14 23 1.1E-29
8 g13172.t3 PRINTS PR00190 Actin signature 39 50 1.1E-29
6 g13172.t3 PRINTS PR00190 Actin signature 51 73 1.1E-29
4 g13172.t3 PRINTS PR00190 Actin signature 106 119 1.1E-29
5 g13172.t3 PRINTS PR00190 Actin signature 131 150 1.1E-29
7 g13172.t3 PRINTS PR00190 Actin signature 227 243 1.1E-29
1 g13172.t3 Pfam PF00022 Actin 4 374 4.0E-99
16 g13172.t3 ProSitePatterns PS01132 Actins and actin-related proteins signature. 95 107 -
17 g13172.t3 SMART SM00268 actin_3 2 377 1.0E-171
11 g13172.t3 SUPERFAMILY SSF53067 Actin-like ATPase domain 4 144 2.17E-45
10 g13172.t3 SUPERFAMILY SSF53067 Actin-like ATPase domain 137 374 1.43E-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

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.

Raw TPM values