Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin-5C.

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 g14309 g14309.t8 isoform g14309.t8 36551599 36553062
chr_1 g14309 g14309.t8 exon g14309.t8.exon1 36551599 36551649
chr_1 g14309 g14309.t8 TTS g14309.t8 36551615 36551615
chr_1 g14309 g14309.t8 exon g14309.t8.exon2 36551727 36553062
chr_1 g14309 g14309.t8 cds g14309.t8.CDS1 36551932 36553062
chr_1 g14309 g14309.t8 TSS g14309.t8 NA NA

Sequences

>g14309.t8 Gene=g14309 Length=1387
ATGTGTGACGAAGAAGTTGCTGCATTGGTCGTTGACAATGGATCAGGAATGTGCAAAGCC
GGTTTTGCTGGTGATGATGCACCACGTGCCGTTTTCCCATCAATTGTCGGTCGTCCACGT
CATCAAGGCGTTATGGTCGGTATGGGACAAAAGGACTCATATGTTGGTGATGAGGCTCAA
AGCAAAAGAGGTATTCTTACCTTGAAATATCCAATTGAACACGGTATTGTTACAAACTGG
GATGATATGGAAAAGATCTGGCATCATACTTTCTACAATGAACTCCGTGTTGCACCTGAA
GAACATCCAGTCTTGCTTACCGAAGCTCCATTAAATCCAAAAGCAAATCGTGAAAAGATG
ACACAAATTATGTTCGAGACATTCAACACACCAGCTATGTATGTTGCAATTCAAGCTGTC
CTCTCATTGTATGCCTCAGGTCGTACAACTGGTATTGTTTTGGATTCTGGTGATGGTGTT
TCACACACAGTTCCAATTTACGAAGGTTATGCTTTGCCACATGCTATCCTTCGTCTTGAT
TTGGCCGGTCGTGATTTGACAGATTATTTGATGAAAATCTTAACCGAACGTGGATACTCA
TTCACAACCACTGCCGAACGTGAAATTGTTCGTGATATCAAAGAAAAATTGTGCTATGTT
GCACTTGACTTTGAACAAGAAATGGCAACAGCTGCTTCATCAAGCTCATTGGAGAAATCA
TATGAATTGCCTGATGGACAAGTCATCACAATCGGAAATGAACGATTCCGTTGTCCAGAA
GCATTGTTCCAGCCATCATTCTTGGGTATGGAAGCATGTGGTATTCACGAGACAACATAC
AATTCAATCATGAAGTGTGACGTTGATATCCGTAAAGACTTGTATGCCAACACAGTCTTG
TCAGGTGGCACAACAATGTACCCAGGTATCGCTGATCGTATGCAAAAGGAAATTACAGCA
TTAGCTCCATCAACAATGAAGATCAAAATTATTGCACCACCAGAACGTAAATACTCAGTC
TGGATCGGAGGTTCAATTTTGGCATCGCTCTCAACCTTCCAACAAATGTGGATCAGCAAA
CAAGAATATGATGAATCAGGCCCATCAATTGTCCACAGAAAATGCTTCTAAATTAATTAT
AATTGTAATCAATTACCACCTTTAAGTCGTCGACATCAAGATCTTCAACCACAGAAACTC
AAAAGACAATTGCATTTTTCACAGTTGAAATTCCATTCATTACATTCCACCACTTACAAC
ATCAACTTTAAGAAAACATGTATTGTCAAAAATATTTTTTGCTCTTTTCTTTTCTATTAT
GAAAACAACATTTAAAATGAATAAAAAGAAAAAGCTTCAAATTTCAAATTCATATAAAAT
TTTTCTT

>g14309.t8 Gene=g14309 Length=376
MCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM
TQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLD
LAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKS
YELPDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCDVDIRKDLYANTVL
SGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISK
QEYDESGPSIVHRKCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14309.t8 CDD cd00012 NBD_sugar-kinase_HSP70_actin 9 182 5.37165E-20
14 g14309.t8 Gene3D G3DSA:3.30.420.40 - 9 372 1.6E-192
13 g14309.t8 Gene3D G3DSA:3.30.420.40 - 139 339 1.6E-192
12 g14309.t8 Gene3D G3DSA:3.90.640.10 Actin; Chain A 181 273 1.6E-192
2 g14309.t8 PANTHER PTHR11937:SF162 ACTIN, INDIRECT FLIGHT MUSCLE-LIKE PROTEIN 1 375 1.5E-257
3 g14309.t8 PANTHER PTHR11937 ACTIN 1 375 1.5E-257
6 g14309.t8 PRINTS PR00190 Actin signature 27 36 4.7E-58
8 g14309.t8 PRINTS PR00190 Actin signature 50 61 4.7E-58
9 g14309.t8 PRINTS PR00190 Actin signature 62 84 4.7E-58
5 g14309.t8 PRINTS PR00190 Actin signature 116 129 4.7E-58
4 g14309.t8 PRINTS PR00190 Actin signature 141 160 4.7E-58
7 g14309.t8 PRINTS PR00190 Actin signature 237 253 4.7E-58
1 g14309.t8 Pfam PF00022 Actin 4 376 1.9E-150
18 g14309.t8 ProSitePatterns PS00406 Actins signature 1. 54 64 -
17 g14309.t8 ProSitePatterns PS01132 Actins and actin-related proteins signature. 105 117 -
16 g14309.t8 ProSitePatterns PS00432 Actins signature 2. 357 365 -
19 g14309.t8 SMART SM00268 actin_3 6 376 7.2E-243
11 g14309.t8 SUPERFAMILY SSF53067 Actin-like ATPase domain 5 154 8.17E-67
10 g14309.t8 SUPERFAMILY SSF53067 Actin-like ATPase domain 148 376 2.16E-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