General information for g11440.t5
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.t5 | TSS | g11440.t5 | 16252413 | 16252413 |
| chr_1 | g11440 | g11440.t5 | isoform | g11440.t5 | 16252527 | 16258404 |
| chr_1 | g11440 | g11440.t5 | exon | g11440.t5.exon1 | 16252527 | 16252538 |
| chr_1 | g11440 | g11440.t5 | exon | g11440.t5.exon2 | 16254218 | 16254348 |
| chr_1 | g11440 | g11440.t5 | exon | g11440.t5.exon3 | 16256201 | 16256362 |
| chr_1 | g11440 | g11440.t5 | cds | g11440.t5.CDS1 | 16256291 | 16256362 |
| chr_1 | g11440 | g11440.t5 | exon | g11440.t5.exon4 | 16256424 | 16256678 |
| chr_1 | g11440 | g11440.t5 | cds | g11440.t5.CDS2 | 16256424 | 16256678 |
| chr_1 | g11440 | g11440.t5 | exon | g11440.t5.exon5 | 16256739 | 16256781 |
| chr_1 | g11440 | g11440.t5 | cds | g11440.t5.CDS3 | 16256739 | 16256781 |
| chr_1 | g11440 | g11440.t5 | exon | g11440.t5.exon6 | 16256840 | 16256950 |
| chr_1 | g11440 | g11440.t5 | cds | g11440.t5.CDS4 | 16256840 | 16256950 |
| chr_1 | g11440 | g11440.t5 | exon | g11440.t5.exon7 | 16257347 | 16257432 |
| chr_1 | g11440 | g11440.t5 | cds | g11440.t5.CDS5 | 16257347 | 16257432 |
| chr_1 | g11440 | g11440.t5 | exon | g11440.t5.exon8 | 16257548 | 16257640 |
| chr_1 | g11440 | g11440.t5 | cds | g11440.t5.CDS6 | 16257548 | 16257640 |
| chr_1 | g11440 | g11440.t5 | exon | g11440.t5.exon9 | 16257698 | 16258404 |
| chr_1 | g11440 | g11440.t5 | cds | g11440.t5.CDS7 | 16257698 | 16258402 |
| chr_1 | g11440 | g11440.t5 | TTS | g11440.t5 | NA | NA |
Sequences
>g11440.t5 Gene=g11440 Length=1600
TCTGTAAAACAGGAAAAAAATGATGGATCAAAATGGATTGTATGCTGAAGAATATGGTGA
AAATGGATATATGGAGCAGGAAGAAGAGTGGGAGCGGGAAGGTCTGCTAGATCCAGCATG
GGAGAAGCAACAGAAAAAGGCAAACCTTTACCGCATGGTGCAACAGTCATTTGAGAAAAG
CCGGAACTTCAATCGAAAACATTGAAGATGATTTCCGCAATGGTCTTAAATTGATGCTTC
TTTTGGAAGTCATTTCTGGTGAAACATTACCAAAACCTGATCGTGGCAAGATGCGTTTCC
ACAAAATTGCAAATGTGAACAAAGCTCTTGATTTTATCGCATCAAAAGGTGTTAAACTTG
TCTCAATTGGTGCTGAAGAAATTGTCGATGGAAACTTGAAAATGACTTTAGGTATGATTT
GGACCATCATTTTAAGATTTGCCATCCAAGACATTTCTGTTGAGGAAATGACAGCTAAAG
AGGGCTTATTGCTTTGGTGTCAACGCAAAACTGCTCCATACAAGAATGTTAATGTGCAAA
ATTTCCATCTCAGTTTCAAGGACGGTTTAGCTTTTTGCGCATTGATTCATCGTCATCGTC
CAGACTTGATCGATTATTCAAAATTGTCAAAGGACAATCCATTGGAGAATTTGAATACTG
CATTCGACGTTGCAGAAAAATACTTGGATATTCCAAGAATGTTGGATCCAGATGATTTAC
AAAACACTGCAATGCCTGATGAACGTGCTGTTATGACTTATGTCTCATCTTATTATCATT
GCTTTAGTGGCGCACAAAAGGCTGAAACTGCAGCTAACCGTATTTGCAAAGTTTTGAAAG
TCAATCAAGAAAATGAAAGACTTATGGAAGAGTATGAGCGTCTTGCATCTGATCTTCTTG
AATGGATTCGTCGTACAATGCCATGGTTAGCATCACGTCATTCCGACAGTACACTAGCTG
GCGTTCAAAAGAAACTTGAAGAGTACCGCACATACAGACGCAAACATAAGCCACCACGTG
TCGAGCAAAAAGCAAAATTGGAAACCAACTTCAATACTCTTCAAACTAAATTACGTCTTT
CAAATAGACCCGCTTATATGCCAACAGAAGGCAAAATGGTTTCAGATATCGCCAATGCAT
GGAAAAATTTAGAATTGGCAGAAAAAGCCTTCGAGGAATGGCTCTTAGCTGAGACTATGC
GTCTGGAACGCTTAGAACACTTGGCACAAAAGTTTAAGCACAAGGCCGATACACATGAAG
AATGGACTCGTGGAAAAGAAGAAATGCTTCAATCTCAAGATTATCGCAGTTGTCGCTTGT
ATGAATTGAAGGCTTTGAAAAAGAAGCACGAAGCATTCGAGTCTGATTTGGCTGCTCATC
AAGATCGCGTTGAACAAATTGCTGCCATCGCTCAAGAACTCAACACATTGGAATATCACG
ATTGTGTAACAGTAAATGCCCGTTGCCAACGCATTTGTGATCAATGGGATCGCTTGGGCG
CATTGACACAACGTCGTCGTCAAGCATTGGATGACTCTGAAAGAGTTCTCGAAAAGATTG
ATTTGCTTCATTTGGAATTTGCCAAACGTGCTGCACCATT
>g11440.t5 Gene=g11440 Length=455
MLLLEVISGETLPKPDRGKMRFHKIANVNKALDFIASKGVKLVSIGAEEIVDGNLKMTLG
MIWTIILRFAIQDISVEEMTAKEGLLLWCQRKTAPYKNVNVQNFHLSFKDGLAFCALIHR
HRPDLIDYSKLSKDNPLENLNTAFDVAEKYLDIPRMLDPDDLQNTAMPDERAVMTYVSSY
YHCFSGAQKAETAANRICKVLKVNQENERLMEEYERLASDLLEWIRRTMPWLASRHSDST
LAGVQKKLEEYRTYRRKHKPPRVEQKAKLETNFNTLQTKLRLSNRPAYMPTEGKMVSDIA
NAWKNLELAEKAFEEWLLAETMRLERLEHLAQKFKHKADTHEEWTRGKEEMLQSQDYRSC
RLYELKALKKKHEAFESDLAAHQDRVEQIAAIAQELNTLEYHDCVTVNARCQRICDQWDR
LGALTQRRRQALDDSERVLEKIDLLHLEFAKRAAP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g11440.t5 | CDD | cd00014 | CH | 3 | 70 | 9.23886E-14 |
| 17 | g11440.t5 | CDD | cd00014 | CH | 81 | 182 | 6.14754E-26 |
| 16 | g11440.t5 | CDD | cd00176 | SPEC | 330 | 448 | 1.78721E-20 |
| 14 | g11440.t5 | Coils | Coil | Coil | 200 | 227 | - |
| 15 | g11440.t5 | Coils | Coil | Coil | 365 | 385 | - |
| 10 | g11440.t5 | Gene3D | G3DSA:1.10.418.10 | - | 1 | 76 | 3.5E-27 |
| 11 | g11440.t5 | Gene3D | G3DSA:1.10.418.10 | - | 77 | 194 | 1.0E-49 |
| 12 | g11440.t5 | Gene3D | G3DSA:1.20.58.60 | - | 200 | 325 | 1.3E-52 |
| 13 | g11440.t5 | Gene3D | G3DSA:1.20.58.60 | - | 326 | 440 | 1.9E-35 |
| 5 | g11440.t5 | PANTHER | PTHR23167:SF25 | ALPHA-ACTININ, SARCOMERIC-LIKE PROTEIN | 29 | 455 | 1.7E-271 |
| 6 | g11440.t5 | PANTHER | PTHR23167 | CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED | 29 | 455 | 1.7E-271 |
| 3 | g11440.t5 | Pfam | PF00307 | Calponin homology (CH) domain | 3 | 70 | 8.1E-11 |
| 4 | g11440.t5 | Pfam | PF00307 | Calponin homology (CH) domain | 80 | 185 | 1.3E-26 |
| 2 | g11440.t5 | Pfam | PF00435 | Spectrin repeat | 210 | 317 | 1.3E-12 |
| 1 | g11440.t5 | Pfam | PF00435 | Spectrin repeat | 329 | 433 | 1.5E-23 |
| 19 | g11440.t5 | ProSitePatterns | PS00020 | Actinin-type actin-binding domain signature 2. | 42 | 66 | - |
| 25 | g11440.t5 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 1 | 70 | 17.159 |
| 24 | g11440.t5 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 79 | 185 | 25.733 |
| 20 | g11440.t5 | SMART | SM00033 | ch_5 | 3 | 68 | 0.077 |
| 21 | g11440.t5 | SMART | SM00033 | ch_5 | 81 | 180 | 1.4E-25 |
| 22 | g11440.t5 | SMART | SM00150 | SPEC_4 | 212 | 318 | 1.3 |
| 23 | g11440.t5 | SMART | SM00150 | SPEC_4 | 332 | 433 | 1.1E-22 |
| 7 | g11440.t5 | SUPERFAMILY | SSF47576 | Calponin-homology domain, CH-domain | 3 | 184 | 2.09E-68 |
| 9 | g11440.t5 | SUPERFAMILY | SSF46966 | Spectrin repeat | 201 | 324 | 3.01E-33 |
| 8 | g11440.t5 | SUPERFAMILY | SSF46966 | Spectrin repeat | 325 | 434 | 1.13E-24 |
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