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.t18 isoform g14309.t18 36551667 36554119
chr_1 g14309 g14309.t18 exon g14309.t18.exon1 36551667 36552044
chr_1 g14309 g14309.t18 TTS g14309.t18 36551672 36551672
chr_1 g14309 g14309.t18 cds g14309.t18.CDS1 36551932 36552044
chr_1 g14309 g14309.t18 exon g14309.t18.exon2 36552126 36553070
chr_1 g14309 g14309.t18 cds g14309.t18.CDS2 36552126 36553062
chr_1 g14309 g14309.t18 exon g14309.t18.exon3 36553948 36554119
chr_1 g14309 g14309.t18 TSS g14309.t18 36554119 36554119

Sequences

>g14309.t18 Gene=g14309 Length=1495
ACTTTGAATTGAGTTGTTGAAGAGTTTAGACGTTTTCTGTGAACGGTCTTTTGAATCATT
TTTTCCAATAAAAAATTAATTAAATCAATAGTGCTGTGTTTTAAAATTGCCGTAAAAGCA
TTCTCAAATCACCAATACTTTCTTTATTGTGAAATTTAAGGACTAAAACAAGAAATCAAA
ATGTGTGACGAAGAAGTTGCTGCATTGGTCGTTGACAATGGATCAGGAATGTGCAAAGCC
GGTTTTGCTGGTGATGATGCACCACGTGCCGTTTTCCCATCAATTGTCGGTCGTCCACGT
CATCAAGGCGTTATGGTCGGTATGGGACAAAAGGACTCATATGTTGGTGATGAGGCTCAA
AGCAAAAGAGGTATTCTTACCTTGAAATATCCAATTGAACACGGTATTGTTACAAACTGG
GATGATATGGAAAAGATCTGGCATCATACTTTCTACAATGAACTCCGTGTTGCACCTGAA
GAACATCCAGTCTTGCTTACCGAAGCTCCATTAAATCCAAAAGCAAATCGTGAAAAGATG
ACACAAATTATGTTCGAGACATTCAACACACCAGCTATGTATGTTGCAATTCAAGCTGTC
CTCTCATTGTATGCCTCAGGTCGTACAACTGGTATTGTTTTGGATTCTGGTGATGGTGTT
TCACACACAGTTCCAATTTACGAAGGTTATGCTTTGCCACATGCTATCCTTCGTCTTGAT
TTGGCCGGTCGTGATTTGACAGATTATTTGATGAAAATCTTAACCGAACGTGGATACTCA
TTCACAACCACTGCCGAACGTGAAATTGTTCGTGATATCAAAGAAAAATTGTGCTATGTT
GCACTTGACTTTGAACAAGAAATGGCAACAGCTGCTTCATCAAGCTCATTGGAGAAATCA
TATGAATTGCCTGATGGACAAGTCATCACAATCGGAAATGAACGATTCCGTTGTCCAGAA
GCATTGTTCCAGCCATCATTCTTGGGTATGGAAGCATGTGGTATTCACGAGACAACATAC
AATTCAATCATGAAGTGTGACGTTGATATCCGTAAAGACTTGTATGCCAACACAGTCTTG
TCAGGTGGCACAACAATGTACCCAGGTATCGCTGATCTCTGGATCGGAGGTTCAATTTTG
GCATCGCTCTCAACCTTCCAACAAATGTGGATCAGCAAACAAGAATATGATGAATCAGGC
CCATCAATTGTCCACAGAAAATGCTTCTAAATTAATTATAATTGTAATCAATTACCACCT
TTAAGTCGTCGACATCAAGATCTTCAACCACAGAAACTCAAAAGACAATTGCATTTTTCA
CAGTTGAAATTCCATTCATTACATTCCACCACTTACAACATCAACTTTAAGAAAACATGT
ATTGTCAAAAATATTTTTTGCTCTTTTCTTTTCTATTATGAAAACAACATTTAAATTTAA
TTTAATTATTATATTACACTACTTTCTCAAAGATCATGAATTTATCACTCAAAAA

>g14309.t18 Gene=g14309 Length=349
MCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM
TQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLD
LAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKS
YELPDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCDVDIRKDLYANTVL
SGGTTMYPGIADLWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g14309.t18 CDD cd00012 NBD_sugar-kinase_HSP70_actin 9 182 6.33284E-20
18 g14309.t18 Gene3D G3DSA:3.30.420.40 - 9 138 1.0E-157
16 g14309.t18 Gene3D G3DSA:3.30.420.40 - 139 308 1.0E-157
15 g14309.t18 Gene3D G3DSA:3.90.640.10 Actin; Chain A 181 273 1.0E-157
17 g14309.t18 Gene3D G3DSA:3.30.420.40 - 309 349 2.5E-17
4 g14309.t18 PANTHER PTHR11937:SF162 ACTIN, INDIRECT FLIGHT MUSCLE-LIKE PROTEIN 1 312 7.1E-231
6 g14309.t18 PANTHER PTHR11937 ACTIN 1 312 7.1E-231
3 g14309.t18 PANTHER PTHR11937:SF162 ACTIN, INDIRECT FLIGHT MUSCLE-LIKE PROTEIN 313 348 7.1E-231
5 g14309.t18 PANTHER PTHR11937 ACTIN 313 348 7.1E-231
9 g14309.t18 PRINTS PR00190 Actin signature 27 36 3.4E-58
11 g14309.t18 PRINTS PR00190 Actin signature 50 61 3.4E-58
12 g14309.t18 PRINTS PR00190 Actin signature 62 84 3.4E-58
8 g14309.t18 PRINTS PR00190 Actin signature 116 129 3.4E-58
7 g14309.t18 PRINTS PR00190 Actin signature 141 160 3.4E-58
10 g14309.t18 PRINTS PR00190 Actin signature 237 253 3.4E-58
2 g14309.t18 Pfam PF00022 Actin 4 312 8.4E-115
1 g14309.t18 Pfam PF00022 Actin 314 349 1.8E-16
22 g14309.t18 ProSitePatterns PS00406 Actins signature 1. 54 64 -
21 g14309.t18 ProSitePatterns PS01132 Actins and actin-related proteins signature. 105 117 -
20 g14309.t18 ProSitePatterns PS00432 Actins signature 2. 330 338 -
23 g14309.t18 SMART SM00268 actin_3 6 349 8.6E-210
14 g14309.t18 SUPERFAMILY SSF53067 Actin-like ATPase domain 5 154 6.98E-67
13 g14309.t18 SUPERFAMILY SSF53067 Actin-like ATPase domain 148 349 9.97E-86

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