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.t2 TSS g11440.t2 16254217 16254217
chr_1 g11440 g11440.t2 isoform g11440.t2 16254225 16259725
chr_1 g11440 g11440.t2 exon g11440.t2.exon1 16254225 16254344
chr_1 g11440 g11440.t2 cds g11440.t2.CDS1 16254225 16254344
chr_1 g11440 g11440.t2 exon g11440.t2.exon2 16256201 16256362
chr_1 g11440 g11440.t2 cds g11440.t2.CDS2 16256201 16256362
chr_1 g11440 g11440.t2 exon g11440.t2.exon3 16256424 16256678
chr_1 g11440 g11440.t2 cds g11440.t2.CDS3 16256424 16256678
chr_1 g11440 g11440.t2 exon g11440.t2.exon4 16256739 16256781
chr_1 g11440 g11440.t2 cds g11440.t2.CDS4 16256739 16256781
chr_1 g11440 g11440.t2 exon g11440.t2.exon5 16256840 16256950
chr_1 g11440 g11440.t2 cds g11440.t2.CDS5 16256840 16256950
chr_1 g11440 g11440.t2 exon g11440.t2.exon6 16257055 16257140
chr_1 g11440 g11440.t2 cds g11440.t2.CDS6 16257055 16257140
chr_1 g11440 g11440.t2 exon g11440.t2.exon7 16257548 16257640
chr_1 g11440 g11440.t2 cds g11440.t2.CDS7 16257548 16257640
chr_1 g11440 g11440.t2 exon g11440.t2.exon8 16257698 16258404
chr_1 g11440 g11440.t2 cds g11440.t2.CDS8 16257698 16258404
chr_1 g11440 g11440.t2 exon g11440.t2.exon9 16258475 16259102
chr_1 g11440 g11440.t2 cds g11440.t2.CDS9 16258475 16259102
chr_1 g11440 g11440.t2 exon g11440.t2.exon10 16259168 16259497
chr_1 g11440 g11440.t2 cds g11440.t2.CDS10 16259168 16259497
chr_1 g11440 g11440.t2 exon g11440.t2.exon11 16259567 16259725
chr_1 g11440 g11440.t2 cds g11440.t2.CDS11 16259567 16259725
chr_1 g11440 g11440.t2 TTS g11440.t2 16260296 16260296

Sequences

>g11440.t2 Gene=g11440 Length=2694
ATGATGGATCAAAATGGATTGTATGCTGAAGAATATGGTGAAAATGGATATATGGAGCAG
GAAGAAGAGTGGGAGCGGGAAGGTCTGCTAGATCCAGCATGGGAGAAGCAACAGAAAAAG
ACCTTTACCGCATGGTGCAACAGTCATTTGAGAAAAGCCGGAACTTCAATCGAAAACATT
GAAGATGATTTCCGCAATGGTCTTAAATTGATGCTTCTTTTGGAAGTCATTTCTGGTGAA
ACATTACCAAAACCTGATCGTGGCAAGATGCGTTTCCACAAAATTGCAAATGTGAACAAA
GCTCTTGATTTTATCGCATCAAAAGGTGTTAAACTTGTCTCAATTGGTGCTGAAGAAATT
GTCGATGGAAACTTGAAAATGACTTTAGGTATGATTTGGACCATCATTTTAAGATTTGCC
ATCCAAGACATTTCTGTTGAGGAAATGACAGCTAAAGAGGGCTTATTGCTTTGGTGTCAA
CGCAAAACTGCTCCATACAAGAATGTTAATGTGCAAAATTTCCATCTCAGTTTCAAGGAC
GGTTTAGCTTTTTGCGCATTGATTCATCGTCATCGTCCAGACTTGATCGATTATTCAAAA
TTGTCAAAGGACAATCCATTGGAGAATTTGAATACTGCATTCGACGTTGCAGAAAAATAC
TTGGATATTCCAAGAATGTTGGATCCAGATGATTTGATCAATACACCTAAACCGGACGAA
AGAGCAATCATGACATACGTGTCATGTTATTATCATGCTTTCCAAGGCGCTCAACAGGCT
GAAACTGCAGCTAACCGTATTTGCAAAGTTTTGAAAGTCAATCAAGAAAATGAAAGACTT
ATGGAAGAGTATGAGCGTCTTGCATCTGATCTTCTTGAATGGATTCGTCGTACAATGCCA
TGGTTAGCATCACGTCATTCCGACAGTACACTAGCTGGCGTTCAAAAGAAACTTGAAGAG
TACCGCACATACAGACGCAAACATAAGCCACCACGTGTCGAGCAAAAAGCAAAATTGGAA
ACCAACTTCAATACTCTTCAAACTAAATTACGTCTTTCAAATAGACCCGCTTATATGCCA
ACAGAAGGCAAAATGGTTTCAGATATCGCCAATGCATGGAAAAATTTAGAATTGGCAGAA
AAAGCCTTCGAGGAATGGCTCTTAGCTGAGACTATGCGTCTGGAACGCTTAGAACACTTG
GCACAAAAGTTTAAGCACAAGGCCGATACACATGAAGAATGGACTCGTGGAAAAGAAGAA
ATGCTTCAATCTCAAGATTATCGCAGTTGTCGCTTGTATGAATTGAAGGCTTTGAAAAAG
AAGCACGAAGCATTCGAGTCTGATTTGGCTGCTCATCAAGATCGCGTTGAACAAATTGCT
GCCATCGCTCAAGAACTCAACACATTGGAATATCACGATTGTGTAACAGTAAATGCCCGT
TGCCAACGCATTTGTGATCAATGGGATCGCTTGGGCGCATTGACACAACGTCGTCGTCAA
GCATTGGATGACTCTGAAAGAGTTCTCGAAAAGATTGATTTGCTTCATTTGGAATTTGCC
AAACGTGCTGCACCATTTAACAATTGGTTAGACGGTGCTCGCGAAGACTTAGTCGACATG
TTCATTGTTCATACAATGGAAGAAATTCAAGGACTTATCACAGCTCACGATCAATTCAAA
GCTACATTAGGTGAAGCCGATAAGGAATATAATCTCATTGTTGGATTGGTTCGTGATGTT
GAAGGATTGGTCAATCAATACCAAATTGCAAATGGATTAGAGAATCCATACACTACACTC
ACCGCTAGAGATTTAACATCAAAATGGGCTGATGTCAAGACATTAGTTCCATCTCGCGAT
CAAACTCTTGCCATGGAACTTAAGAAGCAACAAAATAATGAAATGTTACGTCGTCAATTT
GCTGAAAAGGCAAACAATGTCGGTCCATGGATTGAAAAACAAATGGACGCTGTCAGCGCT
ATTGGCATGTCAATCAGTGGATCATTAGAAGAACAATTGCACAGATTGAAGGAATATGAA
CAGGCAGTTTATGCTTACAAACCACATATTGAAGAATTGGAAAAGATTCATCAAGCAGTA
CAAGAATCTATGATCTTTGAGAATCGCTACACTAACTACACAATGGAAACATTACGTGTT
GGATGGGAACAGCTTTTAACATCAATTAATAGAAATATCAATGAAGTTGAGAATCAAATT
CTCACACGTGACTCAAAAGGAATCACACAAGAACAGTTGACAGAATTCCGCTCAAGCTTC
AATCACTTTGATAAGAATCGCACTGGTCGCTTAGCTCCAGAAGAATTCAAGTCATGTTTG
GTATCAATTGGATACTCAATTGGAAAGGACAGACAAGGAGAATTAGATTTCCAACGCATC
CTCGCTGTTGTTGATCCAAACAGCACTGGTTATGTACACTTTGACGCTTTTCTTGACTTT
ATGACACGCGAGAGTACCGATACCGACACTGCTGAACAAGTTATTGATTCATTTAGAATT
TTGGCATCTGATAAGCCCTACATTCTTCCTGATGAACTTCGACGTGAATTACCACCAGAT
CAAGCTGAATATTGTATCCAAAGAATGCCACCATACAAAGGACCAGGTGCTGTACCAGGA
GCTCTTGATTACATGTCATTCAGTACTGCTCTTTATGGCGAGTCTGATCTGTAA

>g11440.t2 Gene=g11440 Length=897
MMDQNGLYAEEYGENGYMEQEEEWEREGLLDPAWEKQQKKTFTAWCNSHLRKAGTSIENI
EDDFRNGLKLMLLLEVISGETLPKPDRGKMRFHKIANVNKALDFIASKGVKLVSIGAEEI
VDGNLKMTLGMIWTIILRFAIQDISVEEMTAKEGLLLWCQRKTAPYKNVNVQNFHLSFKD
GLAFCALIHRHRPDLIDYSKLSKDNPLENLNTAFDVAEKYLDIPRMLDPDDLINTPKPDE
RAIMTYVSCYYHAFQGAQQAETAANRICKVLKVNQENERLMEEYERLASDLLEWIRRTMP
WLASRHSDSTLAGVQKKLEEYRTYRRKHKPPRVEQKAKLETNFNTLQTKLRLSNRPAYMP
TEGKMVSDIANAWKNLELAEKAFEEWLLAETMRLERLEHLAQKFKHKADTHEEWTRGKEE
MLQSQDYRSCRLYELKALKKKHEAFESDLAAHQDRVEQIAAIAQELNTLEYHDCVTVNAR
CQRICDQWDRLGALTQRRRQALDDSERVLEKIDLLHLEFAKRAAPFNNWLDGAREDLVDM
FIVHTMEEIQGLITAHDQFKATLGEADKEYNLIVGLVRDVEGLVNQYQIANGLENPYTTL
TARDLTSKWADVKTLVPSRDQTLAMELKKQQNNEMLRRQFAEKANNVGPWIEKQMDAVSA
IGMSISGSLEEQLHRLKEYEQAVYAYKPHIEELEKIHQAVQESMIFENRYTNYTMETLRV
GWEQLLTSINRNINEVENQILTRDSKGITQEQLTEFRSSFNHFDKNRTGRLAPEEFKSCL
VSIGYSIGKDRQGELDFQRILAVVDPNSTGYVHFDAFLDFMTRESTDTDTAEQVIDSFRI
LASDKPYILPDELRRELPPDQAEYCIQRMPPYKGPGAVPGALDYMSFSTALYGESDL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
32 g11440.t2 CDD cd00014 CH 38 140 6.94829E-25
31 g11440.t2 CDD cd00014 CH 151 255 1.58956E-27
29 g11440.t2 CDD cd00176 SPEC 282 505 1.13909E-19
28 g11440.t2 CDD cd00176 SPEC 400 627 3.19571E-31
27 g11440.t2 CDD cd00176 SPEC 518 740 4.69416E-15
30 g11440.t2 CDD cd00051 EFh 755 822 4.18863E-11
25 g11440.t2 Coils Coil Coil 270 297 -
26 g11440.t2 Coils Coil Coil 435 455 -
24 g11440.t2 Coils Coil Coil 719 739 -
16 g11440.t2 Gene3D G3DSA:1.10.418.10 - 22 146 2.4E-45
17 g11440.t2 Gene3D G3DSA:1.10.418.10 - 147 264 5.0E-51
21 g11440.t2 Gene3D G3DSA:1.20.58.60 - 270 395 3.9E-52
20 g11440.t2 Gene3D G3DSA:1.20.58.60 - 396 507 5.6E-35
19 g11440.t2 Gene3D G3DSA:1.20.58.60 - 508 631 2.7E-49
18 g11440.t2 Gene3D G3DSA:1.20.58.60 - 632 744 3.0E-49
22 g11440.t2 Gene3D G3DSA:1.10.238.10 - 745 827 1.5E-16
23 g11440.t2 Gene3D G3DSA:1.10.238.10 - 829 897 1.3E-30
8 g11440.t2 PANTHER PTHR23167:SF25 ALPHA-ACTININ, SARCOMERIC-LIKE PROTEIN 86 897 0.0
9 g11440.t2 PANTHER PTHR23167 CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED 86 897 0.0
6 g11440.t2 Pfam PF00307 Calponin homology (CH) domain 37 140 4.2E-24
7 g11440.t2 Pfam PF00307 Calponin homology (CH) domain 150 255 4.9E-27
2 g11440.t2 Pfam PF00435 Spectrin repeat 280 387 3.7E-12
4 g11440.t2 Pfam PF00435 Spectrin repeat 399 503 4.3E-23
1 g11440.t2 Pfam PF00435 Spectrin repeat 516 623 1.7E-12
3 g11440.t2 Pfam PF00435 Spectrin repeat 637 737 9.6E-12
5 g11440.t2 Pfam PF08726 Ca2+ insensitive EF hand 827 893 8.4E-28
34 g11440.t2 ProSitePatterns PS00019 Actinin-type actin-binding domain signature 1. 38 47 -
35 g11440.t2 ProSitePatterns PS00020 Actinin-type actin-binding domain signature 2. 112 136 -
33 g11440.t2 ProSitePatterns PS00018 EF-hand calcium-binding domain. 764 776 -
47 g11440.t2 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 36 140 26.657
48 g11440.t2 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 149 255 26.74
46 g11440.t2 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 751 786 11.975
45 g11440.t2 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 792 827 9.715
39 g11440.t2 SMART SM00033 ch_5 38 138 4.4E-26
38 g11440.t2 SMART SM00033 ch_5 151 250 7.2E-24
43 g11440.t2 SMART SM00150 SPEC_4 282 388 1.3
41 g11440.t2 SMART SM00150 SPEC_4 402 503 1.1E-22
44 g11440.t2 SMART SM00150 SPEC_4 517 624 2.8E-4
42 g11440.t2 SMART SM00150 SPEC_4 638 737 0.25
36 g11440.t2 SMART SM00054 efh_1 755 783 0.0038
37 g11440.t2 SMART SM00054 efh_1 796 824 0.38
40 g11440.t2 SMART SM01184 efhand_Ca_insen_2 827 893 2.2E-41
10 g11440.t2 SUPERFAMILY SSF47576 Calponin-homology domain, CH-domain 15 255 2.23E-88
15 g11440.t2 SUPERFAMILY SSF46966 Spectrin repeat 271 394 9.16E-33
14 g11440.t2 SUPERFAMILY SSF46966 Spectrin repeat 395 504 3.27E-24
13 g11440.t2 SUPERFAMILY SSF46966 Spectrin repeat 508 628 1.7E-24
12 g11440.t2 SUPERFAMILY SSF46966 Spectrin repeat 632 744 1.7E-21
11 g11440.t2 SUPERFAMILY SSF47473 EF-hand 745 893 4.65E-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

Pathway

  • This transcript belongs to the following pathways

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