General information for g11440.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alpha-actinin, sarcomeric.
Parent gene
- The parent gene g11440 is located on chr_1: 16259725..16260443 (+ strand)
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.t11 | isoform | g11440.t11 | 16253610 | 16257768 |
| chr_1 | g11440 | g11440.t11 | exon | g11440.t11.exon1 | 16253610 | 16253727 |
| chr_1 | g11440 | g11440.t11 | exon | g11440.t11.exon2 | 16254218 | 16254331 |
| chr_1 | g11440 | g11440.t11 | cds | g11440.t11.CDS1 | 16254323 | 16254331 |
| chr_1 | g11440 | g11440.t11 | exon | g11440.t11.exon3 | 16256201 | 16256362 |
| chr_1 | g11440 | g11440.t11 | cds | g11440.t11.CDS2 | 16256201 | 16256362 |
| chr_1 | g11440 | g11440.t11 | exon | g11440.t11.exon4 | 16256424 | 16256678 |
| chr_1 | g11440 | g11440.t11 | cds | g11440.t11.CDS3 | 16256424 | 16256678 |
| chr_1 | g11440 | g11440.t11 | exon | g11440.t11.exon5 | 16256739 | 16256781 |
| chr_1 | g11440 | g11440.t11 | cds | g11440.t11.CDS4 | 16256739 | 16256781 |
| chr_1 | g11440 | g11440.t11 | exon | g11440.t11.exon6 | 16256840 | 16256950 |
| chr_1 | g11440 | g11440.t11 | cds | g11440.t11.CDS5 | 16256840 | 16256950 |
| chr_1 | g11440 | g11440.t11 | exon | g11440.t11.exon7 | 16257055 | 16257140 |
| chr_1 | g11440 | g11440.t11 | cds | g11440.t11.CDS6 | 16257055 | 16257140 |
| chr_1 | g11440 | g11440.t11 | exon | g11440.t11.exon8 | 16257548 | 16257640 |
| chr_1 | g11440 | g11440.t11 | cds | g11440.t11.CDS7 | 16257548 | 16257640 |
| chr_1 | g11440 | g11440.t11 | exon | g11440.t11.exon9 | 16257698 | 16257768 |
| chr_1 | g11440 | g11440.t11 | cds | g11440.t11.CDS8 | 16257698 | 16257766 |
| chr_1 | g11440 | g11440.t11 | TSS | g11440.t11 | NA | NA |
| chr_1 | g11440 | g11440.t11 | TTS | g11440.t11 | NA | NA |
Sequences
>g11440.t11 Gene=g11440 Length=1053
AATTTAAAAATATCATCGTCGTGATTCTCTTTAAAAAACGTAAAAATGAAGGCAAAAATT
TTTGTTATTTTTAGTTTAGTTTTGAGTTGGATACCAACGCGAGCGGAACTTAAAACACGA
AAAAAATGATGGATCAAAATGGATTGTATGCTGAAGAATATGGTGAAAATGGATATATGG
AGCAGGAAGAAGAGTGGGAGCGGGAAGGTCTGCTAGATCCAGCATGGGAGAAACCTTTAC
CGCATGGTGCAACAGTCATTTGAGAAAAGCCGGAACTTCAATCGAAAACATTGAAGATGA
TTTCCGCAATGGTCTTAAATTGATGCTTCTTTTGGAAGTCATTTCTGGTGAAACATTACC
AAAACCTGATCGTGGCAAGATGCGTTTCCACAAAATTGCAAATGTGAACAAAGCTCTTGA
TTTTATCGCATCAAAAGGTGTTAAACTTGTCTCAATTGGTGCTGAAGAAATTGTCGATGG
AAACTTGAAAATGACTTTAGGTATGATTTGGACCATCATTTTAAGATTTGCCATCCAAGA
CATTTCTGTTGAGGAAATGACAGCTAAAGAGGGCTTATTGCTTTGGTGTCAACGCAAAAC
TGCTCCATACAAGAATGTTAATGTGCAAAATTTCCATCTCAGTTTCAAGGACGGTTTAGC
TTTTTGCGCATTGATTCATCGTCATCGTCCAGACTTGATCGATTATTCAAAATTGTCAAA
GGACAATCCATTGGAGAATTTGAATACTGCATTCGACGTTGCAGAAAAATACTTGGATAT
TCCAAGAATGTTGGATCCAGATGATTTGATCAATACACCTAAACCGGACGAAAGAGCAAT
CATGACATACGTGTCATGTTATTATCATGCTTTCCAAGGCGCTCAACAGGCTGAAACTGC
AGCTAACCGTATTTGCAAAGTTTTGAAAGTCAATCAAGAAAATGAAAGACTTATGGAAGA
GTATGAGCGTCTTGCATCTGATCTTCTTGAATGGATTCGTCGTACAATGCCATGGTTAGC
ATCACGTCATTCCGACAGTACACTAGCTGGCGT
>g11440.t11 Gene=g11440 Length=276
MGETFTAWCNSHLRKAGTSIENIEDDFRNGLKLMLLLEVISGETLPKPDRGKMRFHKIAN
VNKALDFIASKGVKLVSIGAEEIVDGNLKMTLGMIWTIILRFAIQDISVEEMTAKEGLLL
WCQRKTAPYKNVNVQNFHLSFKDGLAFCALIHRHRPDLIDYSKLSKDNPLENLNTAFDVA
EKYLDIPRMLDPDDLINTPKPDERAIMTYVSCYYHAFQGAQQAETAANRICKVLKVNQEN
ERLMEEYERLASDLLEWIRRTMPWLASRHSDSTLAG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11440.t11 | CDD | cd00014 | CH | 1 | 103 | 9.62309E-25 |
| 11 | g11440.t11 | CDD | cd00014 | CH | 114 | 218 | 1.04946E-28 |
| 10 | g11440.t11 | Coils | Coil | Coil | 233 | 260 | - |
| 7 | g11440.t11 | Gene3D | G3DSA:1.10.418.10 | - | 2 | 109 | 5.1E-42 |
| 8 | g11440.t11 | Gene3D | G3DSA:1.10.418.10 | - | 110 | 227 | 6.0E-52 |
| 9 | g11440.t11 | Gene3D | G3DSA:1.20.58.60 | - | 233 | 276 | 1.1E-13 |
| 3 | g11440.t11 | PANTHER | PTHR11915 | SPECTRIN/FILAMIN RELATED CYTOSKELETAL PROTEIN | 3 | 274 | 9.6E-175 |
| 4 | g11440.t11 | PANTHER | PTHR11915:SF432 | ALPHA-ACTININ-3 | 3 | 274 | 9.6E-175 |
| 1 | g11440.t11 | Pfam | PF00307 | Calponin homology (CH) domain | 3 | 103 | 1.7E-23 |
| 2 | g11440.t11 | Pfam | PF00307 | Calponin homology (CH) domain | 113 | 218 | 6.4E-28 |
| 13 | g11440.t11 | ProSitePatterns | PS00020 | Actinin-type actin-binding domain signature 2. | 75 | 99 | - |
| 17 | g11440.t11 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 1 | 103 | 25.761 |
| 16 | g11440.t11 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 112 | 218 | 26.74 |
| 14 | g11440.t11 | SMART | SM00033 | ch_5 | 1 | 101 | 6.4E-25 |
| 15 | g11440.t11 | SMART | SM00033 | ch_5 | 114 | 213 | 7.2E-24 |
| 5 | g11440.t11 | SUPERFAMILY | SSF47576 | Calponin-homology domain, CH-domain | 3 | 218 | 9.05E-84 |
| 6 | g11440.t11 | SUPERFAMILY | SSF46966 | Spectrin repeat | 234 | 275 | 2.59E-8 |
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. There were no conditions that were differentially expressed