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.t5 TSS g13172.t5 28322010 28322010
chr_1 g13172 g13172.t5 isoform g13172.t5 28322103 28323890
chr_1 g13172 g13172.t5 exon g13172.t5.exon1 28322103 28322368
chr_1 g13172 g13172.t5 cds g13172.t5.CDS1 28322312 28322368
chr_1 g13172 g13172.t5 exon g13172.t5.exon2 28322868 28323890
chr_1 g13172 g13172.t5 cds g13172.t5.CDS2 28322868 28323890
chr_1 g13172 g13172.t5 TTS g13172.t5 28324096 28324096

Sequences

>g13172.t5 Gene=g13172 Length=1289
ATGGATGCACAAGGAAGAAACGTTATAGTTTGCGATAATGGCACAGGTGTAAGTATTTTA
AGCGTATATTTGCGAAAATATTAAATTTGCGCAAATTGGGTTGGGTTTGTTGCTGATAAT
AATTTTTATCACTAATCTCCATTATTCATTTACAGTTTGTAAAATGTGGATATGCTGGAA
GCAATTTCCCAGCACATATCTTTCCATCAATGGTTGGCAGGCCAACAATTCGAGCCGTAA
ATAAAATAGGAGATATTGAAGTAAAAGATTTAATGGTAGGCGATGAAGCATCGCAATTAC
GATCAATGCTTGAAATTTCATATCCTATGGAAAACGGAATGGTTAGAAACTGGGAAGACA
TGTGTCACGTGTGGGATTATACATTTGGTCCGAAAAAGATGAACATTGATCCTACAAATA
CAAAAATTCTATTGACTGAACCACCACTGAATCCATTAAAAAATCGTGAAAAGATGATTG
AAGTGATGTTTGAAAAATATGGTTTTCATTCAACTTATATTGCAATTCAAGCTGTACTGA
CTCTTTACGCACAAGGTCTCATTTCGGGCGTTGTCATCGATTCAGGCGATGGTGTAACAC
ATATTTGCCCAGTTTATGAATCATATGCACTGCCACATTTAACAAAAAGATTGGATATTG
CTGGTCGTGATATTACAAAGTATCTTATTAAGCTATTGCTCCTTCGTGGCTATGCATTCA
ATCATTCTGCTGATTTCGAGACTGTTCGTATGATGAAAGAAAAATTGTGTTATATCGGTT
ATGATATTGAAATGGAACAAAAGTTGGCATTAGAAACGACTGTTCTTGTTGAATCATATA
CATTGCCAGATGGTCGTGTCATTAAAGTTGGTGGTGAGCGATTTGAAGCTCCTGAAGCAC
TTTTCCAGCCTCACTTGATAAATGTTGAAGGACAGGGAATTGCTGAATTAGTTTTTAATA
CAATTCAAGCTGCCGATATAGACATGCGTCCGGAACTTTATAAAAGAATTGTATTATCGG
GTGGGTCTACAATGTATCCGGGTCTTCCCTCTCGTCTTGAACGCGAAATTAAGCAATTAT
ACCTTGAGAGAGTGTTAAAAAATGACATTGATAAACTTTCGAAATTCAAAATTCGAATTG
ATGACCCACCAAGACGAAAGGATATGGTTTTTATTGGAGGAGCAGTTCTTGCTGGTTTAA
ATAAGAACAAAGATGAATTCTGGATGTCAAAGCAAGAGTATCAAGAAATGGGCTTGAAAG
TTCTCTCTAAATGGGGAGCAAGAGCATAA

>g13172.t5 Gene=g13172 Length=359
MVGRPTIRAVNKIGDIEVKDLMVGDEASQLRSMLEISYPMENGMVRNWEDMCHVWDYTFG
PKKMNIDPTNTKILLTEPPLNPLKNREKMIEVMFEKYGFHSTYIAIQAVLTLYAQGLISG
VVIDSGDGVTHICPVYESYALPHLTKRLDIAGRDITKYLIKLLLLRGYAFNHSADFETVR
MMKEKLCYIGYDIEMEQKLALETTVLVESYTLPDGRVIKVGGERFEAPEALFQPHLINVE
GQGIAELVFNTIQAADIDMRPELYKRIVLSGGSTMYPGLPSRLEREIKQLYLERVLKNDI
DKLSKFKIRIDDPPRRKDMVFIGGAVLAGLNKNKDEFWMSKQEYQEMGLKVLSKWGARA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g13172.t5 CDD cd00012 NBD_sugar-kinase_HSP70_actin 37 151 5.25772E-13
13 g13172.t5 Gene3D G3DSA:3.30.420.40 - 2 348 7.9E-134
12 g13172.t5 Gene3D G3DSA:3.30.420.40 - 107 325 7.9E-134
11 g13172.t5 Gene3D G3DSA:3.90.640.10 Actin; Chain A 151 239 7.9E-134
2 g13172.t5 PANTHER PTHR11937:SF149 ACTIN-RELATED PROTEIN 2-A-RELATED 3 355 5.2E-196
3 g13172.t5 PANTHER PTHR11937 ACTIN 3 355 5.2E-196
6 g13172.t5 PRINTS PR00190 Actin signature 18 29 9.3E-27
8 g13172.t5 PRINTS PR00190 Actin signature 30 52 9.3E-27
5 g13172.t5 PRINTS PR00190 Actin signature 85 98 9.3E-27
4 g13172.t5 PRINTS PR00190 Actin signature 110 129 9.3E-27
7 g13172.t5 PRINTS PR00190 Actin signature 206 222 9.3E-27
1 g13172.t5 Pfam PF00022 Actin 9 353 2.9E-92
15 g13172.t5 ProSitePatterns PS01132 Actins and actin-related proteins signature. 74 86 -
16 g13172.t5 SMART SM00268 actin_3 1 356 5.8E-153
10 g13172.t5 SUPERFAMILY SSF53067 Actin-like ATPase domain 5 123 1.04E-36
9 g13172.t5 SUPERFAMILY SSF53067 Actin-like ATPase domain 116 353 1.23E-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 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.

Raw TPM values