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.t1 TTS g9607.t1 4261965 4261965
chr_1 g9607 g9607.t1 isoform g9607.t1 4262387 4263909
chr_1 g9607 g9607.t1 exon g9607.t1.exon1 4262387 4262530
chr_1 g9607 g9607.t1 cds g9607.t1.CDS1 4262387 4262530
chr_1 g9607 g9607.t1 exon g9607.t1.exon2 4262590 4262826
chr_1 g9607 g9607.t1 cds g9607.t1.CDS2 4262590 4262826
chr_1 g9607 g9607.t1 exon g9607.t1.exon3 4262886 4263347
chr_1 g9607 g9607.t1 cds g9607.t1.CDS3 4262886 4263347
chr_1 g9607 g9607.t1 exon g9607.t1.exon4 4263409 4263583
chr_1 g9607 g9607.t1 cds g9607.t1.CDS4 4263409 4263583
chr_1 g9607 g9607.t1 exon g9607.t1.exon5 4263666 4263730
chr_1 g9607 g9607.t1 cds g9607.t1.CDS5 4263666 4263730
chr_1 g9607 g9607.t1 exon g9607.t1.exon6 4263862 4263909
chr_1 g9607 g9607.t1 cds g9607.t1.CDS6 4263862 4263909
chr_1 g9607 g9607.t1 TSS g9607.t1 4263984 4263984

Sequences

>g9607.t1 Gene=g9607 Length=1131
ATGGAACCGTATGATGTAATTGTTAATCAACCAGTAGTTATTGATAATGGATCAGGAATA
ATTAAGGCTGGCTTTGCTGGTGATCAAATTCCTAAATGCATTTTTCCCAATTATGTGGGA
CGACCAAAACATGTACGAGTGATGGCTGGTGCTTTAGAAGGAGATCTTTTTGTTGGTCAA
AGAGCTGATGATCATCGTGGACTTCTTAGCATAAAATATCCTATGGAACATGGTATAATA
GAAGATTGGAATGATATGGAAAGAATCTGGACGCACATATATGGCAAAGACCAGCTTTCT
ACTTTCTCAGAAGAACATCCGGTTCTTCTAACAGAAGCACCATTAAATCCTCGAAAAAAT
CGTGAAAAGTCAGCAGAAATATTTTTTGAGACTTTCAACGTTCCTGCTCTCTTTGTATCA
ATGCAGGCTGTTTTAAGTTTGTATGCGACAGGAAGAGTGACTGGTGTGGTTTTGGATGCT
GGTGATGGCGTTACTCATGCAGTTCCAATTTATGAAGGTTTTGCAATGCCTCACAGTATC
ATGCGAACTGACCTTGCTGGACGTGATGTAACTCGCTACCTAAAAGCACTCATACGAAAA
GAAGGTTTCAATTTTCGCACTACTGCCGAATTCGAAATTGTTAAGATGATAAAAGAAAAA
GTTTGTTATTTGGCCACAAATCTTCAAAAAGAAGAAAATATGGACACAGATAAAATTGGC
TATGTACTGCCTGATGGGAACACTTTAGAGATTGGACAAGCTCGTTTCAGAGCTCCCGAA
GTGCTTTTCAAACCTGATCTGATTGGTGAAGAATGTGAAGGTATTCATGAAGTATTAATG
TACTCAATTCAAAAATCAGATATGGATTTAAGAAAAATGTTATATCAAAACATTGTACTC
TCTGGTGGTTCAACTCTCTTTAAAAACTTTGGAGATCGACTATTACAAGAGATTAAAAAG
AATGTTGCTAAAGACATGAAAATTAGAATCGCAGCTCCTCAAGAGAGACTTTATTCAACA
TGGATGGGTGGCTCAATTTTAGCATCACTTGATACATTCAAAAAAATGTGGATATCAAAA
AGAGAATTTGATGAAGAAGGTCAACGTGCTGTTCATAGGAAGACATTCTAA

>g9607.t1 Gene=g9607 Length=376
MEPYDVIVNQPVVIDNGSGIIKAGFAGDQIPKCIFPNYVGRPKHVRVMAGALEGDLFVGQ
RADDHRGLLSIKYPMEHGIIEDWNDMERIWTHIYGKDQLSTFSEEHPVLLTEAPLNPRKN
REKSAEIFFETFNVPALFVSMQAVLSLYATGRVTGVVLDAGDGVTHAVPIYEGFAMPHSI
MRTDLAGRDVTRYLKALIRKEGFNFRTTAEFEIVKMIKEKVCYLATNLQKEENMDTDKIG
YVLPDGNTLEIGQARFRAPEVLFKPDLIGEECEGIHEVLMYSIQKSDMDLRKMLYQNIVL
SGGSTLFKNFGDRLLQEIKKNVAKDMKIRIAAPQERLYSTWMGGSILASLDTFKKMWISK
REFDEEGQRAVHRKTF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g9607.t1 CDD cd00012 NBD_sugar-kinase_HSP70_actin 12 205 9.61853E-16
13 g9607.t1 Gene3D G3DSA:3.30.420.40 - 12 367 2.1E-160
14 g9607.t1 Gene3D G3DSA:3.30.420.40 - 143 339 2.1E-160
12 g9607.t1 Gene3D G3DSA:3.90.640.10 Actin; Chain A 185 272 2.1E-160
2 g9607.t1 PANTHER PTHR11937 ACTIN 1 375 1.6E-204
3 g9607.t1 PANTHER PTHR11937:SF370 ALPHA-CENTRACTIN 1 375 1.6E-204
9 g9607.t1 PRINTS PR00190 Actin signature 30 39 1.6E-32
8 g9607.t1 PRINTS PR00190 Actin signature 53 64 1.6E-32
5 g9607.t1 PRINTS PR00190 Actin signature 65 87 1.6E-32
7 g9607.t1 PRINTS PR00190 Actin signature 120 133 1.6E-32
6 g9607.t1 PRINTS PR00190 Actin signature 145 164 1.6E-32
4 g9607.t1 PRINTS PR00190 Actin signature 237 253 1.6E-32
1 g9607.t1 Pfam PF00022 Actin 10 375 1.3E-130
16 g9607.t1 ProSitePatterns PS01132 Actins and actin-related proteins signature. 109 121 -
17 g9607.t1 SMART SM00268 actin_3 9 376 5.6E-205
11 g9607.t1 SUPERFAMILY SSF53067 Actin-like ATPase domain 10 158 5.61E-53
10 g9607.t1 SUPERFAMILY SSF53067 Actin-like ATPase domain 151 376 2.43E-78

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

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