Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin, cytoplasmic A3a.

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 g14310 g14310.t24 TTS g14310.t24 36559512 36559512
chr_1 g14310 g14310.t24 isoform g14310.t24 36559621 36561070
chr_1 g14310 g14310.t24 exon g14310.t24.exon1 36559621 36560759
chr_1 g14310 g14310.t24 cds g14310.t24.CDS1 36559621 36560751
chr_1 g14310 g14310.t24 exon g14310.t24.exon2 36561003 36561070
chr_1 g14310 g14310.t24 TSS g14310.t24 36561081 36561081

Sequences

>g14310.t24 Gene=g14310 Length=1207
TCCATCGTTTTGTGACACTTTAGCTTTGGCAAAAAGTGCTTTGAGTTTTCATCAGAATAA
AAAAAAATAAATAAAAATGTGTGACGAAGAAGTTGCTGCATTGGTCGTTGACAATGGATC
AGGAATGTGCAAAGCCGGTTTCGCTGGTGATGATGCACCACGTGCCGTTTTCCCATCAAT
TGTCGGTCGTCCACGTCATCAAGGCGTTATGGTCGGTATGGGACAAAAGGACTCATATGT
TGGTGATGAGGCTCAAAGCAAAAGAGGTATTCTTACCTTGAAATATCCAATTGAACACGG
TATTGTTACAAACTGGGATGATATGGAAAAGATCTGGCATCATACTTTCTACAATGAACT
CCGTGTTGCTCCTGAAGAACATCCAGTCTTGCTTACCGAAGCTCCATTGAATCCAAAAGC
AAATCGTGAAAAGATGACACAAATTATGTTCGAGACATTCAACACACCAGCTATGTATGT
CTCAATTCAAGCTGTCCTCTCATTGTATGCCTCAGGTCGTACAACTGGTATTGTTTTGGA
TTCTGGTGATGGCGTTTCACACACAGTTCCAATTTACGAAGGTTATGCTTTGCCACATGC
TATCCTTCGTCTTGATTTGGCCGGTCGTGATTTAACTGATTTCCTTATGAAAATCTTAAC
CGAACGTGGTTATACTTTCACAACCACTGCCGAACGTGAAATTGTCCGTGATATCAAAGA
AAAATTGTGCTATGTTGCACTTGACTTTGAACAAGAAATGGCAACAGCTGCTTCATCAAG
CTCATTGGAGAAATCATATGAATTGCCTGATGGACAAGTCATCACAATCGGAAATGAACG
ATTCCGTTGTCCAGAAACTCTCTTCCAACCATCATACATTGGTATGGAATCAAATGGAAT
TCACGAAACAACATACAATTCAATCATGAAGTGTGACGTTGATATCCGTAAAGACTTGTA
TGCCAACACAGTCTTGTCAGGTGGCACAACAATGTTCCCAGGTATCGCTGATCGTATGCA
AAAGGAAATTACAGCATTAGCTCCATCAACAATGAAGATCAAAATTATTGCACCACCAGA
ACGTAAATACTCAGTCTGGATCGGAGGTTCAATTTTGGCATCGCTCTCAACCTTCCAACA
AATGTGGATCAGCAAACAAGAATATGATGAATCAGGCCCATCAATTGTCCACAGAAAATG
CTTCTAA

>g14310.t24 Gene=g14310 Length=376
MCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM
TQIMFETFNTPAMYVSIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLD
LAGRDLTDFLMKILTERGYTFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKS
YELPDGQVITIGNERFRCPETLFQPSYIGMESNGIHETTYNSIMKCDVDIRKDLYANTVL
SGGTTMFPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISK
QEYDESGPSIVHRKCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14310.t24 CDD cd00012 NBD_sugar-kinase_HSP70_actin 9 182 5.81848E-20
14 g14310.t24 Gene3D G3DSA:3.30.420.40 - 9 372 3.5E-192
13 g14310.t24 Gene3D G3DSA:3.30.420.40 - 139 339 3.5E-192
12 g14310.t24 Gene3D G3DSA:3.90.640.10 Actin; Chain A 181 273 3.5E-192
2 g14310.t24 PANTHER PTHR11937 ACTIN 1 375 3.6E-253
3 g14310.t24 PANTHER PTHR11937:SF359 ACTIN 1 375 3.6E-253
6 g14310.t24 PRINTS PR00190 Actin signature 27 36 4.7E-58
8 g14310.t24 PRINTS PR00190 Actin signature 50 61 4.7E-58
9 g14310.t24 PRINTS PR00190 Actin signature 62 84 4.7E-58
5 g14310.t24 PRINTS PR00190 Actin signature 116 129 4.7E-58
4 g14310.t24 PRINTS PR00190 Actin signature 141 160 4.7E-58
7 g14310.t24 PRINTS PR00190 Actin signature 237 253 4.7E-58
1 g14310.t24 Pfam PF00022 Actin 4 376 3.8E-150
18 g14310.t24 ProSitePatterns PS00406 Actins signature 1. 54 64 -
17 g14310.t24 ProSitePatterns PS01132 Actins and actin-related proteins signature. 105 117 -
16 g14310.t24 ProSitePatterns PS00432 Actins signature 2. 357 365 -
19 g14310.t24 SMART SM00268 actin_3 6 376 1.5E-241
11 g14310.t24 SUPERFAMILY SSF53067 Actin-like ATPase domain 5 154 1.5E-66
10 g14310.t24 SUPERFAMILY SSF53067 Actin-like ATPase domain 148 376 8.98E-100

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