General information for g11440.t3
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.t3 | isoform | g11440.t3 | 16257364 | 16259725 |
| chr_1 | g11440 | g11440.t3 | exon | g11440.t3.exon1 | 16257364 | 16257432 |
| chr_1 | g11440 | g11440.t3 | cds | g11440.t3.CDS1 | 16257364 | 16257432 |
| chr_1 | g11440 | g11440.t3 | exon | g11440.t3.exon2 | 16257548 | 16257640 |
| chr_1 | g11440 | g11440.t3 | cds | g11440.t3.CDS2 | 16257548 | 16257640 |
| chr_1 | g11440 | g11440.t3 | exon | g11440.t3.exon3 | 16257698 | 16258404 |
| chr_1 | g11440 | g11440.t3 | cds | g11440.t3.CDS3 | 16257698 | 16258404 |
| chr_1 | g11440 | g11440.t3 | exon | g11440.t3.exon4 | 16258475 | 16259102 |
| chr_1 | g11440 | g11440.t3 | cds | g11440.t3.CDS4 | 16258475 | 16259102 |
| chr_1 | g11440 | g11440.t3 | exon | g11440.t3.exon5 | 16259168 | 16259497 |
| chr_1 | g11440 | g11440.t3 | cds | g11440.t3.CDS5 | 16259168 | 16259497 |
| chr_1 | g11440 | g11440.t3 | exon | g11440.t3.exon6 | 16259567 | 16259725 |
| chr_1 | g11440 | g11440.t3 | cds | g11440.t3.CDS6 | 16259567 | 16259725 |
| chr_1 | g11440 | g11440.t3 | TTS | g11440.t3 | 16260296 | 16260296 |
| chr_1 | g11440 | g11440.t3 | TSS | g11440.t3 | NA | NA |
Sequences
>g11440.t3 Gene=g11440 Length=1986
ATGCCTGATGAACGTGCTGTTATGACTTATGTCTCATCTTATTATCATTGCTTTAGTGGC
GCACAAAAGGCTGAAACTGCAGCTAACCGTATTTGCAAAGTTTTGAAAGTCAATCAAGAA
AATGAAAGACTTATGGAAGAGTATGAGCGTCTTGCATCTGATCTTCTTGAATGGATTCGT
CGTACAATGCCATGGTTAGCATCACGTCATTCCGACAGTACACTAGCTGGCGTTCAAAAG
AAACTTGAAGAGTACCGCACATACAGACGCAAACATAAGCCACCACGTGTCGAGCAAAAA
GCAAAATTGGAAACCAACTTCAATACTCTTCAAACTAAATTACGTCTTTCAAATAGACCC
GCTTATATGCCAACAGAAGGCAAAATGGTTTCAGATATCGCCAATGCATGGAAAAATTTA
GAATTGGCAGAAAAAGCCTTCGAGGAATGGCTCTTAGCTGAGACTATGCGTCTGGAACGC
TTAGAACACTTGGCACAAAAGTTTAAGCACAAGGCCGATACACATGAAGAATGGACTCGT
GGAAAAGAAGAAATGCTTCAATCTCAAGATTATCGCAGTTGTCGCTTGTATGAATTGAAG
GCTTTGAAAAAGAAGCACGAAGCATTCGAGTCTGATTTGGCTGCTCATCAAGATCGCGTT
GAACAAATTGCTGCCATCGCTCAAGAACTCAACACATTGGAATATCACGATTGTGTAACA
GTAAATGCCCGTTGCCAACGCATTTGTGATCAATGGGATCGCTTGGGCGCATTGACACAA
CGTCGTCGTCAAGCATTGGATGACTCTGAAAGAGTTCTCGAAAAGATTGATTTGCTTCAT
TTGGAATTTGCCAAACGTGCTGCACCATTTAACAATTGGTTAGACGGTGCTCGCGAAGAC
TTAGTCGACATGTTCATTGTTCATACAATGGAAGAAATTCAAGGACTTATCACAGCTCAC
GATCAATTCAAAGCTACATTAGGTGAAGCCGATAAGGAATATAATCTCATTGTTGGATTG
GTTCGTGATGTTGAAGGATTGGTCAATCAATACCAAATTGCAAATGGATTAGAGAATCCA
TACACTACACTCACCGCTAGAGATTTAACATCAAAATGGGCTGATGTCAAGACATTAGTT
CCATCTCGCGATCAAACTCTTGCCATGGAACTTAAGAAGCAACAAAATAATGAAATGTTA
CGTCGTCAATTTGCTGAAAAGGCAAACAATGTCGGTCCATGGATTGAAAAACAAATGGAC
GCTGTCAGCGCTATTGGCATGTCAATCAGTGGATCATTAGAAGAACAATTGCACAGATTG
AAGGAATATGAACAGGCAGTTTATGCTTACAAACCACATATTGAAGAATTGGAAAAGATT
CATCAAGCAGTACAAGAATCTATGATCTTTGAGAATCGCTACACTAACTACACAATGGAA
ACATTACGTGTTGGATGGGAACAGCTTTTAACATCAATTAATAGAAATATCAATGAAGTT
GAGAATCAAATTCTCACACGTGACTCAAAAGGAATCACACAAGAACAGTTGACAGAATTC
CGCTCAAGCTTCAATCACTTTGATAAGAATCGCACTGGTCGCTTAGCTCCAGAAGAATTC
AAGTCATGTTTGGTATCAATTGGATACTCAATTGGAAAGGACAGACAAGGAGAATTAGAT
TTCCAACGCATCCTCGCTGTTGTTGATCCAAACAGCACTGGTTATGTACACTTTGACGCT
TTTCTTGACTTTATGACACGCGAGAGTACCGATACCGACACTGCTGAACAAGTTATTGAT
TCATTTAGAATTTTGGCATCTGATAAGCCCTACATTCTTCCTGATGAACTTCGACGTGAA
TTACCACCAGATCAAGCTGAATATTGTATCCAAAGAATGCCACCATACAAAGGACCAGGT
GCTGTACCAGGAGCTCTTGATTACATGTCATTCAGTACTGCTCTTTATGGCGAGTCTGAT
CTGTAA
>g11440.t3 Gene=g11440 Length=661
MPDERAVMTYVSSYYHCFSGAQKAETAANRICKVLKVNQENERLMEEYERLASDLLEWIR
RTMPWLASRHSDSTLAGVQKKLEEYRTYRRKHKPPRVEQKAKLETNFNTLQTKLRLSNRP
AYMPTEGKMVSDIANAWKNLELAEKAFEEWLLAETMRLERLEHLAQKFKHKADTHEEWTR
GKEEMLQSQDYRSCRLYELKALKKKHEAFESDLAAHQDRVEQIAAIAQELNTLEYHDCVT
VNARCQRICDQWDRLGALTQRRRQALDDSERVLEKIDLLHLEFAKRAAPFNNWLDGARED
LVDMFIVHTMEEIQGLITAHDQFKATLGEADKEYNLIVGLVRDVEGLVNQYQIANGLENP
YTTLTARDLTSKWADVKTLVPSRDQTLAMELKKQQNNEMLRRQFAEKANNVGPWIEKQMD
AVSAIGMSISGSLEEQLHRLKEYEQAVYAYKPHIEELEKIHQAVQESMIFENRYTNYTME
TLRVGWEQLLTSINRNINEVENQILTRDSKGITQEQLTEFRSSFNHFDKNRTGRLAPEEF
KSCLVSIGYSIGKDRQGELDFQRILAVVDPNSTGYVHFDAFLDFMTRESTDTDTAEQVID
SFRILASDKPYILPDELRRELPPDQAEYCIQRMPPYKGPGAVPGALDYMSFSTALYGESD
L
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g11440.t3 | CDD | cd00176 | SPEC | 46 | 269 | 1.4969E-18 |
| 24 | g11440.t3 | CDD | cd00176 | SPEC | 164 | 391 | 5.7771E-30 |
| 22 | g11440.t3 | CDD | cd00176 | SPEC | 282 | 504 | 3.12464E-14 |
| 25 | g11440.t3 | CDD | cd00051 | EFh | 519 | 586 | 1.84519E-11 |
| 20 | g11440.t3 | Coils | Coil | Coil | 34 | 61 | - |
| 19 | g11440.t3 | Coils | Coil | Coil | 199 | 219 | - |
| 21 | g11440.t3 | Coils | Coil | Coil | 483 | 503 | - |
| 16 | g11440.t3 | Gene3D | G3DSA:1.20.58.60 | - | 34 | 159 | 2.4E-52 |
| 15 | g11440.t3 | Gene3D | G3DSA:1.20.58.60 | - | 160 | 271 | 3.6E-35 |
| 14 | g11440.t3 | Gene3D | G3DSA:1.20.58.60 | - | 272 | 395 | 1.7E-49 |
| 13 | g11440.t3 | Gene3D | G3DSA:1.20.58.60 | - | 396 | 508 | 1.9E-49 |
| 17 | g11440.t3 | Gene3D | G3DSA:1.10.238.10 | - | 509 | 591 | 9.6E-17 |
| 18 | g11440.t3 | Gene3D | G3DSA:1.10.238.10 | - | 593 | 661 | 8.8E-31 |
| 6 | g11440.t3 | PANTHER | PTHR23167:SF25 | ALPHA-ACTININ, SARCOMERIC-LIKE PROTEIN | 2 | 661 | 0.0 |
| 7 | g11440.t3 | PANTHER | PTHR23167 | CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED | 2 | 661 | 0.0 |
| 4 | g11440.t3 | Pfam | PF00435 | Spectrin repeat | 44 | 151 | 2.3E-12 |
| 3 | g11440.t3 | Pfam | PF00435 | Spectrin repeat | 163 | 267 | 2.7E-23 |
| 2 | g11440.t3 | Pfam | PF00435 | Spectrin repeat | 280 | 387 | 1.1E-12 |
| 1 | g11440.t3 | Pfam | PF00435 | Spectrin repeat | 401 | 501 | 6.2E-12 |
| 5 | g11440.t3 | Pfam | PF08726 | Ca2+ insensitive EF hand | 591 | 657 | 5.7E-28 |
| 26 | g11440.t3 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 528 | 540 | - |
| 35 | g11440.t3 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 515 | 550 | 11.975 |
| 34 | g11440.t3 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 556 | 591 | 9.715 |
| 33 | g11440.t3 | SMART | SM00150 | SPEC_4 | 46 | 152 | 1.3 |
| 31 | g11440.t3 | SMART | SM00150 | SPEC_4 | 166 | 267 | 1.1E-22 |
| 30 | g11440.t3 | SMART | SM00150 | SPEC_4 | 281 | 388 | 2.8E-4 |
| 32 | g11440.t3 | SMART | SM00150 | SPEC_4 | 402 | 501 | 0.25 |
| 27 | g11440.t3 | SMART | SM00054 | efh_1 | 519 | 547 | 0.0038 |
| 28 | g11440.t3 | SMART | SM00054 | efh_1 | 560 | 588 | 0.38 |
| 29 | g11440.t3 | SMART | SM01184 | efhand_Ca_insen_2 | 591 | 657 | 2.2E-41 |
| 12 | g11440.t3 | SUPERFAMILY | SSF46966 | Spectrin repeat | 35 | 158 | 6.02E-33 |
| 10 | g11440.t3 | SUPERFAMILY | SSF46966 | Spectrin repeat | 159 | 268 | 2.09E-24 |
| 9 | g11440.t3 | SUPERFAMILY | SSF46966 | Spectrin repeat | 272 | 392 | 9.95E-25 |
| 11 | g11440.t3 | SUPERFAMILY | SSF46966 | Spectrin repeat | 396 | 508 | 1.1E-21 |
| 8 | g11440.t3 | SUPERFAMILY | SSF47473 | EF-hand | 509 | 657 | 2.76E-19 |
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 |
| GO:0005509 | calcium ion 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.
