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.t8 isoform g11440.t8 16253610 16256947
chr_1 g11440 g11440.t8 exon g11440.t8.exon1 16253610 16253727
chr_1 g11440 g11440.t8 exon g11440.t8.exon2 16254218 16254348
chr_1 g11440 g11440.t8 exon g11440.t8.exon3 16256201 16256362
chr_1 g11440 g11440.t8 cds g11440.t8.CDS1 16256291 16256362
chr_1 g11440 g11440.t8 exon g11440.t8.exon4 16256424 16256678
chr_1 g11440 g11440.t8 cds g11440.t8.CDS2 16256424 16256678
chr_1 g11440 g11440.t8 exon g11440.t8.exon5 16256739 16256781
chr_1 g11440 g11440.t8 cds g11440.t8.CDS3 16256739 16256781
chr_1 g11440 g11440.t8 exon g11440.t8.exon6 16256840 16256947
chr_1 g11440 g11440.t8 cds g11440.t8.CDS4 16256840 16256946
chr_1 g11440 g11440.t8 TSS g11440.t8 NA NA
chr_1 g11440 g11440.t8 TTS g11440.t8 NA NA

Sequences

>g11440.t8 Gene=g11440 Length=817
AATTTAAAAATATCATCGTCGTGATTCTCTTTAAAAAACGTAAAAATGAAGGCAAAAATT
TTTGTTATTTTTAGTTTAGTTTTGAGTTGGATACCAACGCGAGCGGAACTTAAAACACGA
AAAAAATGATGGATCAAAATGGATTGTATGCTGAAGAATATGGTGAAAATGGATATATGG
AGCAGGAAGAAGAGTGGGAGCGGGAAGGTCTGCTAGATCCAGCATGGGAGAAGCAACAGA
AAAAGGCAAACCTTTACCGCATGGTGCAACAGTCATTTGAGAAAAGCCGGAACTTCAATC
GAAAACATTGAAGATGATTTCCGCAATGGTCTTAAATTGATGCTTCTTTTGGAAGTCATT
TCTGGTGAAACATTACCAAAACCTGATCGTGGCAAGATGCGTTTCCACAAAATTGCAAAT
GTGAACAAAGCTCTTGATTTTATCGCATCAAAAGGTGTTAAACTTGTCTCAATTGGTGCT
GAAGAAATTGTCGATGGAAACTTGAAAATGACTTTAGGTATGATTTGGACCATCATTTTA
AGATTTGCCATCCAAGACATTTCTGTTGAGGAAATGACAGCTAAAGAGGGCTTATTGCTT
TGGTGTCAACGCAAAACTGCTCCATACAAGAATGTTAATGTGCAAAATTTCCATCTCAGT
TTCAAGGACGGTTTAGCTTTTTGCGCATTGATTCATCGTCATCGTCCAGACTTGATCGAT
TATTCAAAATTGTCAAAGGACAATCCATTGGAGAATTTGAATACTGCATTCGACGTTGCA
GAAAAATACTTGGATATTCCAAGAATGTTGGATCCAG

>g11440.t8 Gene=g11440 Length=159
MLLLEVISGETLPKPDRGKMRFHKIANVNKALDFIASKGVKLVSIGAEEIVDGNLKMTLG
MIWTIILRFAIQDISVEEMTAKEGLLLWCQRKTAPYKNVNVQNFHLSFKDGLAFCALIHR
HRPDLIDYSKLSKDNPLENLNTAFDVAEKYLDIPRMLDP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11440.t8 CDD cd00014 CH 3 70 1.94523E-14
8 g11440.t8 CDD cd00014 CH 81 150 1.62957E-21
7 g11440.t8 Gene3D G3DSA:1.10.418.10 - 1 76 4.7E-28
6 g11440.t8 Gene3D G3DSA:1.10.418.10 - 77 159 2.6E-37
3 g11440.t8 PANTHER PTHR11915 SPECTRIN/FILAMIN RELATED CYTOSKELETAL PROTEIN 1 158 2.8E-100
4 g11440.t8 PANTHER PTHR11915:SF432 ALPHA-ACTININ-3 1 158 2.8E-100
2 g11440.t8 Pfam PF00307 Calponin homology (CH) domain 3 70 1.2E-11
1 g11440.t8 Pfam PF00307 Calponin homology (CH) domain 80 158 1.5E-21
10 g11440.t8 ProSitePatterns PS00020 Actinin-type actin-binding domain signature 2. 42 66 -
14 g11440.t8 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 1 70 17.159
13 g11440.t8 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 79 159 22.526
12 g11440.t8 SMART SM00033 ch_5 3 68 0.077
11 g11440.t8 SMART SM00033 ch_5 81 159 8.8E-10
5 g11440.t8 SUPERFAMILY SSF47576 Calponin-homology domain, CH-domain 3 159 2.3E-59

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