General information for g11440.t14
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.t14 | TSS | g11440.t14 | 16254217 | 16254217 |
| chr_1 | g11440 | g11440.t14 | isoform | g11440.t14 | 16254225 | 16257768 |
| chr_1 | g11440 | g11440.t14 | exon | g11440.t14.exon1 | 16254225 | 16254348 |
| chr_1 | g11440 | g11440.t14 | exon | g11440.t14.exon2 | 16256201 | 16256366 |
| chr_1 | g11440 | g11440.t14 | exon | g11440.t14.exon3 | 16256424 | 16256678 |
| chr_1 | g11440 | g11440.t14 | cds | g11440.t14.CDS1 | 16256520 | 16256678 |
| chr_1 | g11440 | g11440.t14 | exon | g11440.t14.exon4 | 16256739 | 16256781 |
| chr_1 | g11440 | g11440.t14 | cds | g11440.t14.CDS2 | 16256739 | 16256781 |
| chr_1 | g11440 | g11440.t14 | exon | g11440.t14.exon5 | 16256840 | 16256950 |
| chr_1 | g11440 | g11440.t14 | cds | g11440.t14.CDS3 | 16256840 | 16256950 |
| chr_1 | g11440 | g11440.t14 | exon | g11440.t14.exon6 | 16257055 | 16257140 |
| chr_1 | g11440 | g11440.t14 | cds | g11440.t14.CDS4 | 16257055 | 16257140 |
| chr_1 | g11440 | g11440.t14 | exon | g11440.t14.exon7 | 16257548 | 16257640 |
| chr_1 | g11440 | g11440.t14 | cds | g11440.t14.CDS5 | 16257548 | 16257640 |
| chr_1 | g11440 | g11440.t14 | exon | g11440.t14.exon8 | 16257698 | 16257768 |
| chr_1 | g11440 | g11440.t14 | cds | g11440.t14.CDS6 | 16257698 | 16257766 |
| chr_1 | g11440 | g11440.t14 | TTS | g11440.t14 | NA | NA |
Sequences
>g11440.t14 Gene=g11440 Length=949
ATGATGGATCAAAATGGATTGTATGCTGAAGAATATGGTGAAAATGGATATATGGAGCAG
GAAGAAGAGTGGGAGCGGGAAGGTCTGCTAGATCCAGCATGGGAGAAGCAACAGAAAAAG
GCAAACCTTTACCGCATGGTGCAACAGTCATTTGAGAAAAGCCGGAACTTCAATCGAAAA
CATTGAAGATGATTTCCGCAATGGTCTTAAATTGATGCTTCTTTTGGAAGTCATTTCTGG
TGAAACATTACCAAAACCTGATCGTGGCAAGATGCGTTTCCACAAAGTATATTGCAAATG
TGAACAAAGCTCTTGATTTTATCGCATCAAAAGGTGTTAAACTTGTCTCAATTGGTGCTG
AAGAAATTGTCGATGGAAACTTGAAAATGACTTTAGGTATGATTTGGACCATCATTTTAA
GATTTGCCATCCAAGACATTTCTGTTGAGGAAATGACAGCTAAAGAGGGCTTATTGCTTT
GGTGTCAACGCAAAACTGCTCCATACAAGAATGTTAATGTGCAAAATTTCCATCTCAGTT
TCAAGGACGGTTTAGCTTTTTGCGCATTGATTCATCGTCATCGTCCAGACTTGATCGATT
ATTCAAAATTGTCAAAGGACAATCCATTGGAGAATTTGAATACTGCATTCGACGTTGCAG
AAAAATACTTGGATATTCCAAGAATGTTGGATCCAGATGATTTGATCAATACACCTAAAC
CGGACGAAAGAGCAATCATGACATACGTGTCATGTTATTATCATGCTTTCCAAGGCGCTC
AACAGGCTGAAACTGCAGCTAACCGTATTTGCAAAGTTTTGAAAGTCAATCAAGAAAATG
AAAGACTTATGGAAGAGTATGAGCGTCTTGCATCTGATCTTCTTGAATGGATTCGTCGTA
CAATGCCATGGTTAGCATCACGTCATTCCGACAGTACACTAGCTGGCGT
>g11440.t14 Gene=g11440 Length=187
MTLGMIWTIILRFAIQDISVEEMTAKEGLLLWCQRKTAPYKNVNVQNFHLSFKDGLAFCA
LIHRHRPDLIDYSKLSKDNPLENLNTAFDVAEKYLDIPRMLDPDDLINTPKPDERAIMTY
VSCYYHAFQGAQQAETAANRICKVLKVNQENERLMEEYERLASDLLEWIRRTMPWLASRH
SDSTLAG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11440.t14 | CDD | cd00014 | CH | 25 | 129 | 5.02249E-30 |
| 9 | g11440.t14 | Coils | Coil | Coil | 144 | 171 | - |
| 7 | g11440.t14 | Gene3D | G3DSA:1.10.418.10 | - | 19 | 138 | 2.2E-52 |
| 8 | g11440.t14 | Gene3D | G3DSA:1.20.58.60 | - | 144 | 187 | 5.7E-14 |
| 2 | g11440.t14 | PANTHER | PTHR23167:SF25 | ALPHA-ACTININ, SARCOMERIC-LIKE PROTEIN | 1 | 187 | 6.7E-130 |
| 3 | g11440.t14 | PANTHER | PTHR23167 | CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED | 1 | 187 | 6.7E-130 |
| 1 | g11440.t14 | Pfam | PF00307 | Calponin homology (CH) domain | 24 | 129 | 2.4E-28 |
| 12 | g11440.t14 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 23 | 129 | 26.74 |
| 11 | g11440.t14 | SMART | SM00033 | ch_5 | 25 | 124 | 7.2E-24 |
| 4 | g11440.t14 | SUPERFAMILY | SSF47576 | Calponin-homology domain, CH-domain | 1 | 129 | 2.23E-46 |
| 5 | g11440.t14 | SUPERFAMILY | SSF46966 | Spectrin repeat | 145 | 186 | 1.44E-8 |
| 6 | g11440.t14 | 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. There were no conditions that were differentially expressed