Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin-related protein 3.

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 g10194 g10194.t6 TSS g10194.t6 8163978 8163978
chr_1 g10194 g10194.t6 isoform g10194.t6 8164080 8166261
chr_1 g10194 g10194.t6 exon g10194.t6.exon1 8164080 8164123
chr_1 g10194 g10194.t6 cds g10194.t6.CDS1 8164080 8164123
chr_1 g10194 g10194.t6 exon g10194.t6.exon2 8164251 8164431
chr_1 g10194 g10194.t6 cds g10194.t6.CDS2 8164251 8164431
chr_1 g10194 g10194.t6 exon g10194.t6.exon3 8164492 8165343
chr_1 g10194 g10194.t6 cds g10194.t6.CDS3 8164492 8165343
chr_1 g10194 g10194.t6 exon g10194.t6.exon4 8165407 8165490
chr_1 g10194 g10194.t6 cds g10194.t6.CDS4 8165407 8165490
chr_1 g10194 g10194.t6 exon g10194.t6.exon5 8165553 8165945
chr_1 g10194 g10194.t6 cds g10194.t6.CDS5 8165553 8165648
chr_1 g10194 g10194.t6 exon g10194.t6.exon6 8166009 8166261
chr_1 g10194 g10194.t6 TTS g10194.t6 8166263 8166263

Sequences

>g10194.t6 Gene=g10194 Length=1807
ATGACAGGAAGGCTTCCAGCTTGTGTAATTGATGTTGGTACCGGTTATACTAAATTAGGC
TACGCTGCTAATAAAGATCCACAATTTATCTTTCCATCTGCAATTGCCATCAAAGAGAGC
GCTCGTGTTGGTGACCAAACAGCTCGCAGAATAACAAAAGGTGTCGAAGATTTAGATTTT
TATATCGGCGATGAAGCATTTGATGCAACTGGATATGCAGTAAAGTATCCTGTTCGTCAT
GGCTTAGTAGAAGATTGGGATTTAATGGAACGATTTTTGGAACAATGTATTTTCAAATAT
TTACGTGCTGAACCTGGAGATCATCATTTTTTGCTCACTGAACCACCACTCAACACACCC
GAAAATCGTGAATATACTGCCGAGATAATGTTTGAAACATTCAACGTTCCTGGGCTTTAT
ATCGCCGTACAAGCTGTGTTGGCACTGGCTGCCAGTTGGGCTTCTCGTCCTGTTGAAGAA
CGCACACTGACTGGAATTGTGATTGATAGTGGTGATGGTGTCACTCATGTCATTCCAGTT
GCCGAGGGCTATGTTATTGGATCTTGTATCAAGCATATTCCAATCGCTGGTCGAAACATT
ACCTCATTCATTCAAAGCTTATTACGAGAACGAGAGGTGGGCATTCCGCCTGAACAAAGT
CTTGAAACTGCCAAAGCAATTAAAGAACGTTTCTGTTACATATGTCCCGATATTGCAAAA
GAATTTGCAAAATATGATTCAGAACCATCGAAATGGATTAAGACTTATGAAGGTATCAAT
AGTATTACGAAGCAACAATTTAATGTTGATGTAGGATATGAAAGATTCCTTGGTCCAGAA
ATTTTCTTTCATCCTGAATTTTCAAATCCTGACTTTACTACGCCAATATCCGAAATTGTT
GATAATGTCATTCAAAATTGTCCGATCGATGTTCGACGACCATTGTATAATAATATTGTT
TTGAGCGGTGGCTCAACTATGTTTAGAGACTTTGGTAGACGCTTACAGCGTGATATTAAA
AGATCAGTTGATGCTCGACTAAGAATTAGTGAAAATTTAAGTGAGGGAAGAATTAAGCCC
AAACCCATTGATGTGAATGTCATTTCTCACCATATGCAACGTTATGCTGTTTGGTTCGGC
GGAAGCATGTTGGCGTCAACACCTGAATTTTATCAAGTTTGTCATACAAAAGCAGAATAC
GAGGAATATGGTCCTCGCATTTGCCGTTACAATGCAGTATTCGGTACAATGACGTAATTT
TTTTTGTTTGGTGGTCTTGTTTTACATATAGTATATCAACATCAACTTAGACATTCCTAC
TATTGCTGAGCTCAACATCAATCATCAAGAGACACGTTTATTCTATCATTGATAAAAGCT
GAAAATCTTTTTTCTATGAAAATTGTAAAATGCTTTAGAAGACTACCGCCAAATTAATTT
TTTTGGCGACTTATGAACAAATACAAACTTTTTATAATTTCTTTATTTAAAAAGTGAAAG
TAGGAAAAATAGTGAAAATGCCCCATTTGAAATTAAATATACTTATTTTAGCCATATATA
ATATATTTTTTTGTTTCATTCAAAATTTCATTTCACTCTTTACAATATATATTAATCATA
ATTTTTTAAAATGATTCGCGTCTATAGTGAAACATGTTGCATTTCAATTTAAGTTTAAAT
ATTTTTTATATTATTTTAAATTTACAAGTACGCAAAAAAGAACTTTCCGTTTTCATTCTC
TTAAAGTGATTTTTTTTACTCAATAACTTCTTTTAAAAAAGTTTCAAATAAAGAATTGTC
TTTTGTC

>g10194.t6 Gene=g10194 Length=418
MTGRLPACVIDVGTGYTKLGYAANKDPQFIFPSAIAIKESARVGDQTARRITKGVEDLDF
YIGDEAFDATGYAVKYPVRHGLVEDWDLMERFLEQCIFKYLRAEPGDHHFLLTEPPLNTP
ENREYTAEIMFETFNVPGLYIAVQAVLALAASWASRPVEERTLTGIVIDSGDGVTHVIPV
AEGYVIGSCIKHIPIAGRNITSFIQSLLREREVGIPPEQSLETAKAIKERFCYICPDIAK
EFAKYDSEPSKWIKTYEGINSITKQQFNVDVGYERFLGPEIFFHPEFSNPDFTTPISEIV
DNVIQNCPIDVRRPLYNNIVLSGGSTMFRDFGRRLQRDIKRSVDARLRISENLSEGRIKP
KPIDVNVISHHMQRYAVWFGGSMLASTPEFYQVCHTKAEYEEYGPRICRYNAVFGTMT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10194.t6 CDD cd00012 NBD_sugar-kinase_HSP70_actin 9 209 2.032E-11
9 g10194.t6 Gene3D G3DSA:3.30.420.40 - 9 405 1.6E-148
10 g10194.t6 Gene3D G3DSA:3.30.420.40 - 145 386 1.6E-148
8 g10194.t6 Gene3D G3DSA:3.90.640.10 Actin; Chain A 202 300 1.6E-148
2 g10194.t6 PANTHER PTHR11937 ACTIN 6 409 1.3E-218
3 g10194.t6 PANTHER PTHR11937:SF175 ACTIN-RELATED PROTEIN 3 6 409 1.3E-218
1 g10194.t6 Pfam PF00022 Actin 5 409 2.1E-89
7 g10194.t6 ProSitePatterns PS01132 Actins and actin-related proteins signature. 111 123 -
6 g10194.t6 SMART SM00268 actin_3 5 413 7.5E-171
5 g10194.t6 SUPERFAMILY SSF53067 Actin-like ATPase domain 5 155 1.63E-48
4 g10194.t6 SUPERFAMILY SSF53067 Actin-like ATPase domain 162 414 1.3E-79

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: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