Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin-related protein 1.

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 g9607 g9607.t7 TTS g9607.t7 4261965 4261965
chr_1 g9607 g9607.t7 isoform g9607.t7 4262910 4263909
chr_1 g9607 g9607.t7 exon g9607.t7.exon1 4262910 4263347
chr_1 g9607 g9607.t7 cds g9607.t7.CDS1 4262910 4263347
chr_1 g9607 g9607.t7 exon g9607.t7.exon2 4263409 4263583
chr_1 g9607 g9607.t7 cds g9607.t7.CDS2 4263409 4263583
chr_1 g9607 g9607.t7 exon g9607.t7.exon3 4263666 4263730
chr_1 g9607 g9607.t7 cds g9607.t7.CDS3 4263666 4263730
chr_1 g9607 g9607.t7 exon g9607.t7.exon4 4263862 4263909
chr_1 g9607 g9607.t7 cds g9607.t7.CDS4 4263862 4263909
chr_1 g9607 g9607.t7 TSS g9607.t7 4263984 4263984

Sequences

>g9607.t7 Gene=g9607 Length=726
ATGGAACCGTATGATGTAATTGTTAATCAACCAGTAGTTATTGATAATGGATCAGGAATA
ATTAAGGCTGGCTTTGCTGGTGATCAAATTCCTAAATGCATTTTTCCCAATTATGTGGGA
CGACCAAAACATGTACGAGTGATGGCTGGTGCTTTAGAAGGAGATCTTTTTGTTGGTCAA
AGAGCTGATGATCATCGTGGACTTCTTAGCATAAAATATCCTATGGAACATGGTATAATA
GAAGATTGGAATGATATGGAAAGAATCTGGACGCACATATATGGCAAAGACCAGCTTTCT
ACTTTCTCAGAAGAACATCCGGTTCTTCTAACAGAAGCACCATTAAATCCTCGAAAAAAT
CGTGAAAAGTCAGCAGAAATATTTTTTGAGACTTTCAACGTTCCTGCTCTCTTTGTATCA
ATGCAGGCTGTTTTAAGTTTGTATGCGACAGGAAGAGTGACTGGTGTGGTTTTGGATGCT
GGTGATGGCGTTACTCATGCAGTTCCAATTTATGAAGGTTTTGCAATGCCTCACAGTATC
ATGCGAACTGACCTTGCTGGACGTGATGTAACTCGCTACCTAAAAGCACTCATACGAAAA
GAAGGTTTCAATTTTCGCACTACTGCCGAATTCGAAATTGTTAAGATGATAAAAGAAAAA
GTTTGTTATTTGGCCACAAATCTTCAAAAAGAAGAAAATATGGACACAGATAAAATTGGC
TATGTA

>g9607.t7 Gene=g9607 Length=242
MEPYDVIVNQPVVIDNGSGIIKAGFAGDQIPKCIFPNYVGRPKHVRVMAGALEGDLFVGQ
RADDHRGLLSIKYPMEHGIIEDWNDMERIWTHIYGKDQLSTFSEEHPVLLTEAPLNPRKN
REKSAEIFFETFNVPALFVSMQAVLSLYATGRVTGVVLDAGDGVTHAVPIYEGFAMPHSI
MRTDLAGRDVTRYLKALIRKEGFNFRTTAEFEIVKMIKEKVCYLATNLQKEENMDTDKIG
YV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g9607.t7 CDD cd00012 NBD_sugar-kinase_HSP70_actin 12 205 2.79312E-15
13 g9607.t7 Gene3D G3DSA:3.30.420.40 - 7 155 5.9E-63
12 g9607.t7 Gene3D G3DSA:3.30.420.40 - 156 186 1.8E-27
11 g9607.t7 Gene3D G3DSA:3.90.640.10 Actin; Chain A 187 237 1.8E-27
2 g9607.t7 PANTHER PTHR11937 ACTIN 1 241 2.5E-128
3 g9607.t7 PANTHER PTHR11937:SF370 ALPHA-CENTRACTIN 1 241 2.5E-128
8 g9607.t7 PRINTS PR00190 Actin signature 30 39 1.3E-29
7 g9607.t7 PRINTS PR00190 Actin signature 53 64 1.3E-29
4 g9607.t7 PRINTS PR00190 Actin signature 65 87 1.3E-29
6 g9607.t7 PRINTS PR00190 Actin signature 120 133 1.3E-29
5 g9607.t7 PRINTS PR00190 Actin signature 145 164 1.3E-29
1 g9607.t7 Pfam PF00022 Actin 10 236 4.9E-73
15 g9607.t7 ProSitePatterns PS01132 Actins and actin-related proteins signature. 109 121 -
16 g9607.t7 SMART SM00268 actin_3 9 242 1.2E-63
9 g9607.t7 SUPERFAMILY SSF53067 Actin-like ATPase domain 10 158 1.79E-53
10 g9607.t7 SUPERFAMILY SSF53067 Actin-like ATPase domain 151 234 5.55E-25

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.

Raw TPM values