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.t6 TTS g9607.t6 4261965 4261965
chr_1 g9607 g9607.t6 isoform g9607.t6 4262387 4263909
chr_1 g9607 g9607.t6 exon g9607.t6.exon1 4262387 4262826
chr_1 g9607 g9607.t6 cds g9607.t6.CDS1 4262563 4262826
chr_1 g9607 g9607.t6 exon g9607.t6.exon2 4262886 4263347
chr_1 g9607 g9607.t6 cds g9607.t6.CDS2 4262886 4263347
chr_1 g9607 g9607.t6 exon g9607.t6.exon3 4263409 4263583
chr_1 g9607 g9607.t6 cds g9607.t6.CDS3 4263409 4263583
chr_1 g9607 g9607.t6 exon g9607.t6.exon4 4263666 4263730
chr_1 g9607 g9607.t6 cds g9607.t6.CDS4 4263666 4263730
chr_1 g9607 g9607.t6 exon g9607.t6.exon5 4263862 4263909
chr_1 g9607 g9607.t6 cds g9607.t6.CDS5 4263862 4263909
chr_1 g9607 g9607.t6 TSS g9607.t6 4263984 4263984

Sequences

>g9607.t6 Gene=g9607 Length=1190
ATGGAACCGTATGATGTAATTGTTAATCAACCAGTAGTTATTGATAATGGATCAGGAATA
ATTAAGGCTGGCTTTGCTGGTGATCAAATTCCTAAATGCATTTTTCCCAATTATGTGGGA
CGACCAAAACATGTACGAGTGATGGCTGGTGCTTTAGAAGGAGATCTTTTTGTTGGTCAA
AGAGCTGATGATCATCGTGGACTTCTTAGCATAAAATATCCTATGGAACATGGTATAATA
GAAGATTGGAATGATATGGAAAGAATCTGGACGCACATATATGGCAAAGACCAGCTTTCT
ACTTTCTCAGAAGAACATCCGGTTCTTCTAACAGAAGCACCATTAAATCCTCGAAAAAAT
CGTGAAAAGTCAGCAGAAATATTTTTTGAGACTTTCAACGTTCCTGCTCTCTTTGTATCA
ATGCAGGCTGTTTTAAGTTTGTATGCGACAGGAAGAGTGACTGGTGTGGTTTTGGATGCT
GGTGATGGCGTTACTCATGCAGTTCCAATTTATGAAGGTTTTGCAATGCCTCACAGTATC
ATGCGAACTGACCTTGCTGGACGTGATGTAACTCGCTACCTAAAAGCACTCATACGAAAA
GAAGGTTTCAATTTTCGCACTACTGCCGAATTCGAAATTGTTAAGATGATAAAAGAAAAA
GTTTGTTATTTGGCCACAAATCTTCAAAAAGAAGAAAATATGGACACAGATAAAATTGGC
TATGTACTGCCTGATGGGAACACTTTAGAGATTGGACAAGCTCGTTTCAGAGCTCCCGAA
GTGCTTTTCAAACCTGATCTGATTGGTGAAGAATGTGAAGGTATTCATGAAGTATTAATG
TACTCAATTCAAAAATCAGATATGGATTTAAGAAAAATGTTATATCAAAACATTGTACTC
TCTGGTGGTTCAACTCTCTTTAAAAACTTTGGAGATCGACTATTACAAGAGATTAAAAAG
AATGTTGCTAAAGACATGAAAATTAGAGTAAGTGACAAAAAATTGTTTTATTAATAAAAT
TTAATAATGCTTGAATAAATTTTTAGATCGCAGCTCCTCAAGAGAGACTTTATTCAACAT
GGATGGGTGGCTCAATTTTAGCATCACTTGATACATTCAAAAAAATGTGGATATCAAAAA
GAGAATTTGATGAAGAAGGTCAACGTGCTGTTCATAGGAAGACATTCTAA

>g9607.t6 Gene=g9607 Length=337
MEPYDVIVNQPVVIDNGSGIIKAGFAGDQIPKCIFPNYVGRPKHVRVMAGALEGDLFVGQ
RADDHRGLLSIKYPMEHGIIEDWNDMERIWTHIYGKDQLSTFSEEHPVLLTEAPLNPRKN
REKSAEIFFETFNVPALFVSMQAVLSLYATGRVTGVVLDAGDGVTHAVPIYEGFAMPHSI
MRTDLAGRDVTRYLKALIRKEGFNFRTTAEFEIVKMIKEKVCYLATNLQKEENMDTDKIG
YVLPDGNTLEIGQARFRAPEVLFKPDLIGEECEGIHEVLMYSIQKSDMDLRKMLYQNIVL
SGGSTLFKNFGDRLLQEIKKNVAKDMKIRVSDKKLFY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g9607.t6 CDD cd00012 NBD_sugar-kinase_HSP70_actin 12 205 1.50483E-15
14 g9607.t6 Gene3D G3DSA:3.30.420.40 - 12 142 7.5E-142
13 g9607.t6 Gene3D G3DSA:3.30.420.40 - 143 333 7.5E-142
12 g9607.t6 Gene3D G3DSA:3.90.640.10 Actin; Chain A 185 272 7.5E-142
2 g9607.t6 PANTHER PTHR11937 ACTIN 1 332 6.5E-182
3 g9607.t6 PANTHER PTHR11937:SF370 ALPHA-CENTRACTIN 1 332 6.5E-182
9 g9607.t6 PRINTS PR00190 Actin signature 30 39 9.4E-33
8 g9607.t6 PRINTS PR00190 Actin signature 53 64 9.4E-33
5 g9607.t6 PRINTS PR00190 Actin signature 65 87 9.4E-33
7 g9607.t6 PRINTS PR00190 Actin signature 120 133 9.4E-33
6 g9607.t6 PRINTS PR00190 Actin signature 145 164 9.4E-33
4 g9607.t6 PRINTS PR00190 Actin signature 237 253 9.4E-33
1 g9607.t6 Pfam PF00022 Actin 10 333 1.2E-106
16 g9607.t6 ProSitePatterns PS01132 Actins and actin-related proteins signature. 109 121 -
17 g9607.t6 SMART SM00268 actin_3 9 336 7.1E-159
11 g9607.t6 SUPERFAMILY SSF53067 Actin-like ATPase domain 10 158 4.32E-53
10 g9607.t6 SUPERFAMILY SSF53067 Actin-like ATPase domain 151 330 5.87E-58

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