Gene loci information

Transcript annotation

  • This transcript has been annotated as Alpha-actinin, sarcomeric.

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 g11440 g11440.t15 isoform g11440.t15 16256490 16257768
chr_1 g11440 g11440.t15 exon g11440.t15.exon1 16256490 16256678
chr_1 g11440 g11440.t15 cds g11440.t15.CDS1 16256520 16256678
chr_1 g11440 g11440.t15 exon g11440.t15.exon2 16256739 16256781
chr_1 g11440 g11440.t15 cds g11440.t15.CDS2 16256739 16256781
chr_1 g11440 g11440.t15 exon g11440.t15.exon3 16256840 16256950
chr_1 g11440 g11440.t15 cds g11440.t15.CDS3 16256840 16256950
chr_1 g11440 g11440.t15 exon g11440.t15.exon4 16257055 16257140
chr_1 g11440 g11440.t15 cds g11440.t15.CDS4 16257055 16257140
chr_1 g11440 g11440.t15 exon g11440.t15.exon5 16257548 16257640
chr_1 g11440 g11440.t15 cds g11440.t15.CDS5 16257548 16257640
chr_1 g11440 g11440.t15 exon g11440.t15.exon6 16257698 16257768
chr_1 g11440 g11440.t15 cds g11440.t15.CDS6 16257698 16257766
chr_1 g11440 g11440.t15 TSS g11440.t15 NA NA
chr_1 g11440 g11440.t15 TTS g11440.t15 NA NA

Sequences

>g11440.t15 Gene=g11440 Length=593
GCTGAAGAAATTGTCGATGGAAACTTGAAAATGACTTTAGGTATGATTTGGACCATCATT
TTAAGATTTGCCATCCAAGACATTTCTGTTGAGGAAATGACAGCTAAAGAGGGCTTATTG
CTTTGGTGTCAACGCAAAACTGCTCCATACAAGAATGTTAATGTGCAAAATTTCCATCTC
AGTTTCAAGGACGGTTTAGCTTTTTGCGCATTGATTCATCGTCATCGTCCAGACTTGATC
GATTATTCAAAATTGTCAAAGGACAATCCATTGGAGAATTTGAATACTGCATTCGACGTT
GCAGAAAAATACTTGGATATTCCAAGAATGTTGGATCCAGATGATTTGATCAATACACCT
AAACCGGACGAAAGAGCAATCATGACATACGTGTCATGTTATTATCATGCTTTCCAAGGC
GCTCAACAGGCTGAAACTGCAGCTAACCGTATTTGCAAAGTTTTGAAAGTCAATCAAGAA
AATGAAAGACTTATGGAAGAGTATGAGCGTCTTGCATCTGATCTTCTTGAATGGATTCGT
CGTACAATGCCATGGTTAGCATCACGTCATTCCGACAGTACACTAGCTGGCGT

>g11440.t15 Gene=g11440 Length=187
MTLGMIWTIILRFAIQDISVEEMTAKEGLLLWCQRKTAPYKNVNVQNFHLSFKDGLAFCA
LIHRHRPDLIDYSKLSKDNPLENLNTAFDVAEKYLDIPRMLDPDDLINTPKPDERAIMTY
VSCYYHAFQGAQQAETAANRICKVLKVNQENERLMEEYERLASDLLEWIRRTMPWLASRH
SDSTLAG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11440.t15 CDD cd00014 CH 25 129 5.02249E-30
9 g11440.t15 Coils Coil Coil 144 171 -
7 g11440.t15 Gene3D G3DSA:1.10.418.10 - 19 138 2.2E-52
8 g11440.t15 Gene3D G3DSA:1.20.58.60 - 144 187 5.7E-14
2 g11440.t15 PANTHER PTHR23167:SF25 ALPHA-ACTININ, SARCOMERIC-LIKE PROTEIN 1 187 6.7E-130
3 g11440.t15 PANTHER PTHR23167 CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED 1 187 6.7E-130
1 g11440.t15 Pfam PF00307 Calponin homology (CH) domain 24 129 2.4E-28
12 g11440.t15 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 23 129 26.74
11 g11440.t15 SMART SM00033 ch_5 25 124 7.2E-24
4 g11440.t15 SUPERFAMILY SSF47576 Calponin-homology domain, CH-domain 1 129 2.23E-46
5 g11440.t15 SUPERFAMILY SSF46966 Spectrin repeat 145 186 1.44E-8
6 g11440.t15 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -

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:0005515 protein binding MF

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