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.t4 TSS g11440.t4 16252413 16252413
chr_1 g11440 g11440.t4 isoform g11440.t4 16252527 16256781
chr_1 g11440 g11440.t4 exon g11440.t4.exon1 16252527 16252538
chr_1 g11440 g11440.t4 exon g11440.t4.exon2 16254218 16254348
chr_1 g11440 g11440.t4 exon g11440.t4.exon3 16256201 16256362
chr_1 g11440 g11440.t4 cds g11440.t4.CDS1 16256291 16256362
chr_1 g11440 g11440.t4 exon g11440.t4.exon4 16256424 16256678
chr_1 g11440 g11440.t4 cds g11440.t4.CDS2 16256424 16256678
chr_1 g11440 g11440.t4 exon g11440.t4.exon5 16256739 16256781
chr_1 g11440 g11440.t4 cds g11440.t4.CDS3 16256739 16256780
chr_1 g11440 g11440.t4 TTS g11440.t4 NA NA

Sequences

>g11440.t4 Gene=g11440 Length=603
TCTGTAAAACAGGAAAAAAATGATGGATCAAAATGGATTGTATGCTGAAGAATATGGTGA
AAATGGATATATGGAGCAGGAAGAAGAGTGGGAGCGGGAAGGTCTGCTAGATCCAGCATG
GGAGAAGCAACAGAAAAAGGCAAACCTTTACCGCATGGTGCAACAGTCATTTGAGAAAAG
CCGGAACTTCAATCGAAAACATTGAAGATGATTTCCGCAATGGTCTTAAATTGATGCTTC
TTTTGGAAGTCATTTCTGGTGAAACATTACCAAAACCTGATCGTGGCAAGATGCGTTTCC
ACAAAATTGCAAATGTGAACAAAGCTCTTGATTTTATCGCATCAAAAGGTGTTAAACTTG
TCTCAATTGGTGCTGAAGAAATTGTCGATGGAAACTTGAAAATGACTTTAGGTATGATTT
GGACCATCATTTTAAGATTTGCCATCCAAGACATTTCTGTTGAGGAAATGACAGCTAAAG
AGGGCTTATTGCTTTGGTGTCAACGCAAAACTGCTCCATACAAGAATGTTAATGTGCAAA
ATTTCCATCTCAGTTTCAAGGACGGTTTAGCTTTTTGCGCATTGATTCATCGTCATCGTC
CAG

>g11440.t4 Gene=g11440 Length=123
MLLLEVISGETLPKPDRGKMRFHKIANVNKALDFIASKGVKLVSIGAEEIVDGNLKMTLG
MIWTIILRFAIQDISVEEMTAKEGLLLWCQRKTAPYKNVNVQNFHLSFKDGLAFCALIHR
HRP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11440.t4 CDD cd00014 CH 3 70 3.23333E-15
7 g11440.t4 Gene3D G3DSA:1.10.418.10 - 1 76 2.4E-28
8 g11440.t4 Gene3D G3DSA:1.10.418.10 - 77 123 8.2E-20
3 g11440.t4 PANTHER PTHR11915 SPECTRIN/FILAMIN RELATED CYTOSKELETAL PROTEIN 1 123 1.0E-77
4 g11440.t4 PANTHER PTHR11915:SF432 ALPHA-ACTININ-3 1 123 1.0E-77
1 g11440.t4 Pfam PF00307 Calponin homology (CH) domain 3 70 6.1E-12
2 g11440.t4 Pfam PF00307 Calponin homology (CH) domain 80 123 8.3E-11
6 g11440.t4 ProSitePatterns PS00020 Actinin-type actin-binding domain signature 2. 42 66 -
10 g11440.t4 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 1 70 17.159
9 g11440.t4 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 79 123 15.174
5 g11440.t4 SUPERFAMILY SSF47576 Calponin-homology domain, CH-domain 3 123 6.06E-46

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