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.t6 TSS g11440.t6 16252413 16252413
chr_1 g11440 g11440.t6 isoform g11440.t6 16252527 16260443
chr_1 g11440 g11440.t6 exon g11440.t6.exon1 16252527 16252538
chr_1 g11440 g11440.t6 exon g11440.t6.exon2 16254218 16254348
chr_1 g11440 g11440.t6 exon g11440.t6.exon3 16256201 16256362
chr_1 g11440 g11440.t6 cds g11440.t6.CDS1 16256291 16256362
chr_1 g11440 g11440.t6 exon g11440.t6.exon4 16256424 16256678
chr_1 g11440 g11440.t6 cds g11440.t6.CDS2 16256424 16256678
chr_1 g11440 g11440.t6 exon g11440.t6.exon5 16256739 16256781
chr_1 g11440 g11440.t6 cds g11440.t6.CDS3 16256739 16256781
chr_1 g11440 g11440.t6 exon g11440.t6.exon6 16256840 16256950
chr_1 g11440 g11440.t6 cds g11440.t6.CDS4 16256840 16256950
chr_1 g11440 g11440.t6 exon g11440.t6.exon7 16257347 16257432
chr_1 g11440 g11440.t6 cds g11440.t6.CDS5 16257347 16257432
chr_1 g11440 g11440.t6 exon g11440.t6.exon8 16257548 16257640
chr_1 g11440 g11440.t6 cds g11440.t6.CDS6 16257548 16257640
chr_1 g11440 g11440.t6 exon g11440.t6.exon9 16257698 16258404
chr_1 g11440 g11440.t6 cds g11440.t6.CDS7 16257698 16258404
chr_1 g11440 g11440.t6 exon g11440.t6.exon10 16258475 16259102
chr_1 g11440 g11440.t6 cds g11440.t6.CDS8 16258475 16259102
chr_1 g11440 g11440.t6 exon g11440.t6.exon11 16259168 16259497
chr_1 g11440 g11440.t6 cds g11440.t6.CDS9 16259168 16259497
chr_1 g11440 g11440.t6 exon g11440.t6.exon12 16259567 16260443
chr_1 g11440 g11440.t6 cds g11440.t6.CDS10 16259567 16259725
chr_1 g11440 g11440.t6 TTS g11440.t6 NA NA

Sequences

>g11440.t6 Gene=g11440 Length=3435
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
ATTTGCTTCATTTGGAATTTGCCAAACGTGCTGCACCATTTAACAATTGGTTAGACGGTG
CTCGCGAAGACTTAGTCGACATGTTCATTGTTCATACAATGGAAGAAATTCAAGGACTTA
TCACAGCTCACGATCAATTCAAAGCTACATTAGGTGAAGCCGATAAGGAATATAATCTCA
TTGTTGGATTGGTTCGTGATGTTGAAGGATTGGTCAATCAATACCAAATTGCAAATGGAT
TAGAGAATCCATACACTACACTCACCGCTAGAGATTTAACATCAAAATGGGCTGATGTCA
AGACATTAGTTCCATCTCGCGATCAAACTCTTGCCATGGAACTTAAGAAGCAACAAAATA
ATGAAATGTTACGTCGTCAATTTGCTGAAAAGGCAAACAATGTCGGTCCATGGATTGAAA
AACAAATGGACGCTGTCAGCGCTATTGGCATGTCAATCAGTGGATCATTAGAAGAACAAT
TGCACAGATTGAAGGAATATGAACAGGCAGTTTATGCTTACAAACCACATATTGAAGAAT
TGGAAAAGATTCATCAAGCAGTACAAGAATCTATGATCTTTGAGAATCGCTACACTAACT
ACACAATGGAAACATTACGTGTTGGATGGGAACAGCTTTTAACATCAATTAATAGAAATA
TCAATGAAGTTGAGAATCAAATTCTCACACGTGACTCAAAAGGAATCACACAAGAACAGT
TGACAGAATTCCGCTCAAGCTTCAATCACTTTGATAAGAATCGCACTGGTCGCTTAGCTC
CAGAAGAATTCAAGTCATGTTTGGTATCAATTGGATACTCAATTGGAAAGGACAGACAAG
GAGAATTAGATTTCCAACGCATCCTCGCTGTTGTTGATCCAAACAGCACTGGTTATGTAC
ACTTTGACGCTTTTCTTGACTTTATGACACGCGAGAGTACCGATACCGACACTGCTGAAC
AAGTTATTGATTCATTTAGAATTTTGGCATCTGATAAGCCCTACATTCTTCCTGATGAAC
TTCGACGTGAATTACCACCAGATCAAGCTGAATATTGTATCCAAAGAATGCCACCATACA
AAGGACCAGGTGCTGTACCAGGAGCTCTTGATTACATGTCATTCAGTACTGCTCTTTATG
GCGAGTCTGATCTGTAAACATACAATGTTCATATTTGAAGTATATCAAATAACACGAGAA
CTATTTATATAAGCCAAGAATATTTTTATATATAACTATCTCGAAGCGAATGTTTGTCTC
TTTACTTTTGATCGAAAATTTTTGACACATCTCTTTTTGTTTTTAATTTGCATGCGTAAG
TGGAAAAAGTTTTCCGCTGCAACTGAAAAGAAGAAGTAGAAAGAAGCAATCAATTTTTCT
ATCAGAATGTTCATAATTCATTTTAAATTTTTCTTTGTGTTTTTATTGAAAAGAATAATT
TTTTCTGCCTTATGTAGTAATTTAATGTAATTGAACATCAATCATTAAGAAGCGATATTT
TTTATATTTTATTAAACGAATGATGATGATGATAATGATAAAAATCATGAAGCAGCTATA
TTCAAAATTTTATAATAATTCGATGTTTCTGCAAAGAAAGAAAAAATAAGCAAAAAATTG
TAAAAGGATGAAAAGGAGAAGTTTTGATTTCACAATATATATTTTATTTATATTTATTAT
TTTACGAAACATAATGCCATGATGAAATAAAATTTAACTTTTAAAAAGAAACTACACTCA
ATTGCTCATATTTTAAACAACAACATATCTTTTTATTGAATTATTCTCATTAACATTGCA
ATTATAACATGTTTAAAACATTTTACAGTTAATTTTTGGTATTTTTCAGAATCTGATGTT
AAATATTTTAGCTTT

>g11440.t6 Gene=g11440 Length=827
MLLLEVISGETLPKPDRGKMRFHKIANVNKALDFIASKGVKLVSIGAEEIVDGNLKMTLG
MIWTIILRFAIQDISVEEMTAKEGLLLWCQRKTAPYKNVNVQNFHLSFKDGLAFCALIHR
HRPDLIDYSKLSKDNPLENLNTAFDVAEKYLDIPRMLDPDDLQNTAMPDERAVMTYVSSY
YHCFSGAQKAETAANRICKVLKVNQENERLMEEYERLASDLLEWIRRTMPWLASRHSDST
LAGVQKKLEEYRTYRRKHKPPRVEQKAKLETNFNTLQTKLRLSNRPAYMPTEGKMVSDIA
NAWKNLELAEKAFEEWLLAETMRLERLEHLAQKFKHKADTHEEWTRGKEEMLQSQDYRSC
RLYELKALKKKHEAFESDLAAHQDRVEQIAAIAQELNTLEYHDCVTVNARCQRICDQWDR
LGALTQRRRQALDDSERVLEKIDLLHLEFAKRAAPFNNWLDGAREDLVDMFIVHTMEEIQ
GLITAHDQFKATLGEADKEYNLIVGLVRDVEGLVNQYQIANGLENPYTTLTARDLTSKWA
DVKTLVPSRDQTLAMELKKQQNNEMLRRQFAEKANNVGPWIEKQMDAVSAIGMSISGSLE
EQLHRLKEYEQAVYAYKPHIEELEKIHQAVQESMIFENRYTNYTMETLRVGWEQLLTSIN
RNINEVENQILTRDSKGITQEQLTEFRSSFNHFDKNRTGRLAPEEFKSCLVSIGYSIGKD
RQGELDFQRILAVVDPNSTGYVHFDAFLDFMTRESTDTDTAEQVIDSFRILASDKPYILP
DELRRELPPDQAEYCIQRMPPYKGPGAVPGALDYMSFSTALYGESDL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
32 g11440.t6 CDD cd00014 CH 3 70 8.36713E-14
31 g11440.t6 CDD cd00014 CH 81 182 5.30224E-26
28 g11440.t6 CDD cd00176 SPEC 212 435 1.40292E-19
27 g11440.t6 CDD cd00176 SPEC 330 557 4.04959E-31
29 g11440.t6 CDD cd00176 SPEC 448 670 5.20077E-15
30 g11440.t6 CDD cd00051 EFh 685 752 3.60107E-11
25 g11440.t6 Coils Coil Coil 200 227 -
26 g11440.t6 Coils Coil Coil 365 385 -
24 g11440.t6 Coils Coil Coil 649 669 -
16 g11440.t6 Gene3D G3DSA:1.10.418.10 - 1 76 8.2E-27
17 g11440.t6 Gene3D G3DSA:1.10.418.10 - 77 194 2.6E-49
21 g11440.t6 Gene3D G3DSA:1.20.58.60 - 200 325 3.4E-52
20 g11440.t6 Gene3D G3DSA:1.20.58.60 - 326 437 5.0E-35
19 g11440.t6 Gene3D G3DSA:1.20.58.60 - 438 561 2.4E-49
18 g11440.t6 Gene3D G3DSA:1.20.58.60 - 562 674 2.6E-49
23 g11440.t6 Gene3D G3DSA:1.10.238.10 - 675 757 1.3E-16
22 g11440.t6 Gene3D G3DSA:1.10.238.10 - 759 827 1.2E-30
8 g11440.t6 PANTHER PTHR23167:SF25 ALPHA-ACTININ, SARCOMERIC-LIKE PROTEIN 29 827 0.0
9 g11440.t6 PANTHER PTHR23167 CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED 29 827 0.0
6 g11440.t6 Pfam PF00307 Calponin homology (CH) domain 3 70 1.8E-10
7 g11440.t6 Pfam PF00307 Calponin homology (CH) domain 80 185 3.2E-26
4 g11440.t6 Pfam PF00435 Spectrin repeat 210 317 3.3E-12
2 g11440.t6 Pfam PF00435 Spectrin repeat 329 433 3.8E-23
3 g11440.t6 Pfam PF00435 Spectrin repeat 446 553 1.5E-12
1 g11440.t6 Pfam PF00435 Spectrin repeat 567 667 8.6E-12
5 g11440.t6 Pfam PF08726 Ca2+ insensitive EF hand 757 823 7.6E-28
34 g11440.t6 ProSitePatterns PS00020 Actinin-type actin-binding domain signature 2. 42 66 -
33 g11440.t6 ProSitePatterns PS00018 EF-hand calcium-binding domain. 694 706 -
47 g11440.t6 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 1 70 17.159
46 g11440.t6 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 79 185 25.733
45 g11440.t6 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 681 716 11.975
44 g11440.t6 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 722 757 9.715
37 g11440.t6 SMART SM00033 ch_5 3 68 0.077
38 g11440.t6 SMART SM00033 ch_5 81 180 1.4E-25
40 g11440.t6 SMART SM00150 SPEC_4 212 318 1.3
41 g11440.t6 SMART SM00150 SPEC_4 332 433 1.1E-22
42 g11440.t6 SMART SM00150 SPEC_4 447 554 2.8E-4
43 g11440.t6 SMART SM00150 SPEC_4 568 667 0.25
35 g11440.t6 SMART SM00054 efh_1 685 713 0.0038
36 g11440.t6 SMART SM00054 efh_1 726 754 0.38
39 g11440.t6 SMART SM01184 efhand_Ca_insen_2 757 823 2.2E-41
10 g11440.t6 SUPERFAMILY SSF47576 Calponin-homology domain, CH-domain 3 184 6.68E-68
15 g11440.t6 SUPERFAMILY SSF46966 Spectrin repeat 201 324 8.24E-33
14 g11440.t6 SUPERFAMILY SSF46966 Spectrin repeat 325 434 2.88E-24
13 g11440.t6 SUPERFAMILY SSF46966 Spectrin repeat 438 558 1.44E-24
12 g11440.t6 SUPERFAMILY SSF46966 Spectrin repeat 562 674 1.57E-21
11 g11440.t6 SUPERFAMILY SSF47473 EF-hand 675 823 4.12E-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.

Raw TPM values