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.t16 isoform g11440.t16 16256842 16259725
chr_1 g11440 g11440.t16 exon g11440.t16.exon1 16256842 16256950
chr_1 g11440 g11440.t16 cds g11440.t16.CDS1 16256935 16256950
chr_1 g11440 g11440.t16 exon g11440.t16.exon2 16257055 16257140
chr_1 g11440 g11440.t16 cds g11440.t16.CDS2 16257055 16257140
chr_1 g11440 g11440.t16 exon g11440.t16.exon3 16257548 16257640
chr_1 g11440 g11440.t16 cds g11440.t16.CDS3 16257548 16257640
chr_1 g11440 g11440.t16 exon g11440.t16.exon4 16257698 16258404
chr_1 g11440 g11440.t16 cds g11440.t16.CDS4 16257698 16258404
chr_1 g11440 g11440.t16 exon g11440.t16.exon5 16258475 16259102
chr_1 g11440 g11440.t16 cds g11440.t16.CDS5 16258475 16259102
chr_1 g11440 g11440.t16 exon g11440.t16.exon6 16259168 16259497
chr_1 g11440 g11440.t16 cds g11440.t16.CDS6 16259168 16259497
chr_1 g11440 g11440.t16 exon g11440.t16.exon7 16259567 16259725
chr_1 g11440 g11440.t16 cds g11440.t16.CDS7 16259567 16259725
chr_1 g11440 g11440.t16 TTS g11440.t16 16260296 16260296
chr_1 g11440 g11440.t16 TSS g11440.t16 NA NA

Sequences

>g11440.t16 Gene=g11440 Length=2112
TTGATCGATTATTCAAAATTGTCAAAGGACAATCCATTGGAGAATTTGAATACTGCATTC
GACGTTGCAGAAAAATACTTGGATATTCCAAGAATGTTGGATCCAGATGATTTGATCAAT
ACACCTAAACCGGACGAAAGAGCAATCATGACATACGTGTCATGTTATTATCATGCTTTC
CAAGGCGCTCAACAGGCTGAAACTGCAGCTAACCGTATTTGCAAAGTTTTGAAAGTCAAT
CAAGAAAATGAAAGACTTATGGAAGAGTATGAGCGTCTTGCATCTGATCTTCTTGAATGG
ATTCGTCGTACAATGCCATGGTTAGCATCACGTCATTCCGACAGTACACTAGCTGGCGTT
CAAAAGAAACTTGAAGAGTACCGCACATACAGACGCAAACATAAGCCACCACGTGTCGAG
CAAAAAGCAAAATTGGAAACCAACTTCAATACTCTTCAAACTAAATTACGTCTTTCAAAT
AGACCCGCTTATATGCCAACAGAAGGCAAAATGGTTTCAGATATCGCCAATGCATGGAAA
AATTTAGAATTGGCAGAAAAAGCCTTCGAGGAATGGCTCTTAGCTGAGACTATGCGTCTG
GAACGCTTAGAACACTTGGCACAAAAGTTTAAGCACAAGGCCGATACACATGAAGAATGG
ACTCGTGGAAAAGAAGAAATGCTTCAATCTCAAGATTATCGCAGTTGTCGCTTGTATGAA
TTGAAGGCTTTGAAAAAGAAGCACGAAGCATTCGAGTCTGATTTGGCTGCTCATCAAGAT
CGCGTTGAACAAATTGCTGCCATCGCTCAAGAACTCAACACATTGGAATATCACGATTGT
GTAACAGTAAATGCCCGTTGCCAACGCATTTGTGATCAATGGGATCGCTTGGGCGCATTG
ACACAACGTCGTCGTCAAGCATTGGATGACTCTGAAAGAGTTCTCGAAAAGATTGATTTG
CTTCATTTGGAATTTGCCAAACGTGCTGCACCATTTAACAATTGGTTAGACGGTGCTCGC
GAAGACTTAGTCGACATGTTCATTGTTCATACAATGGAAGAAATTCAAGGACTTATCACA
GCTCACGATCAATTCAAAGCTACATTAGGTGAAGCCGATAAGGAATATAATCTCATTGTT
GGATTGGTTCGTGATGTTGAAGGATTGGTCAATCAATACCAAATTGCAAATGGATTAGAG
AATCCATACACTACACTCACCGCTAGAGATTTAACATCAAAATGGGCTGATGTCAAGACA
TTAGTTCCATCTCGCGATCAAACTCTTGCCATGGAACTTAAGAAGCAACAAAATAATGAA
ATGTTACGTCGTCAATTTGCTGAAAAGGCAAACAATGTCGGTCCATGGATTGAAAAACAA
ATGGACGCTGTCAGCGCTATTGGCATGTCAATCAGTGGATCATTAGAAGAACAATTGCAC
AGATTGAAGGAATATGAACAGGCAGTTTATGCTTACAAACCACATATTGAAGAATTGGAA
AAGATTCATCAAGCAGTACAAGAATCTATGATCTTTGAGAATCGCTACACTAACTACACA
ATGGAAACATTACGTGTTGGATGGGAACAGCTTTTAACATCAATTAATAGAAATATCAAT
GAAGTTGAGAATCAAATTCTCACACGTGACTCAAAAGGAATCACACAAGAACAGTTGACA
GAATTCCGCTCAAGCTTCAATCACTTTGATAAGAATCGCACTGGTCGCTTAGCTCCAGAA
GAATTCAAGTCATGTTTGGTATCAATTGGATACTCAATTGGAAAGGACAGACAAGGAGAA
TTAGATTTCCAACGCATCCTCGCTGTTGTTGATCCAAACAGCACTGGTTATGTACACTTT
GACGCTTTTCTTGACTTTATGACACGCGAGAGTACCGATACCGACACTGCTGAACAAGTT
ATTGATTCATTTAGAATTTTGGCATCTGATAAGCCCTACATTCTTCCTGATGAACTTCGA
CGTGAATTACCACCAGATCAAGCTGAATATTGTATCCAAAGAATGCCACCATACAAAGGA
CCAGGTGCTGTACCAGGAGCTCTTGATTACATGTCATTCAGTACTGCTCTTTATGGCGAG
TCTGATCTGTAA

>g11440.t16 Gene=g11440 Length=672
MLDPDDLINTPKPDERAIMTYVSCYYHAFQGAQQAETAANRICKVLKVNQENERLMEEYE
RLASDLLEWIRRTMPWLASRHSDSTLAGVQKKLEEYRTYRRKHKPPRVEQKAKLETNFNT
LQTKLRLSNRPAYMPTEGKMVSDIANAWKNLELAEKAFEEWLLAETMRLERLEHLAQKFK
HKADTHEEWTRGKEEMLQSQDYRSCRLYELKALKKKHEAFESDLAAHQDRVEQIAAIAQE
LNTLEYHDCVTVNARCQRICDQWDRLGALTQRRRQALDDSERVLEKIDLLHLEFAKRAAP
FNNWLDGAREDLVDMFIVHTMEEIQGLITAHDQFKATLGEADKEYNLIVGLVRDVEGLVN
QYQIANGLENPYTTLTARDLTSKWADVKTLVPSRDQTLAMELKKQQNNEMLRRQFAEKAN
NVGPWIEKQMDAVSAIGMSISGSLEEQLHRLKEYEQAVYAYKPHIEELEKIHQAVQESMI
FENRYTNYTMETLRVGWEQLLTSINRNINEVENQILTRDSKGITQEQLTEFRSSFNHFDK
NRTGRLAPEEFKSCLVSIGYSIGKDRQGELDFQRILAVVDPNSTGYVHFDAFLDFMTRES
TDTDTAEQVIDSFRILASDKPYILPDELRRELPPDQAEYCIQRMPPYKGPGAVPGALDYM
SFSTALYGESDL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g11440.t16 CDD cd00176 SPEC 57 280 1.76406E-18
24 g11440.t16 CDD cd00176 SPEC 175 402 7.04409E-30
25 g11440.t16 CDD cd00176 SPEC 293 515 3.74869E-14
26 g11440.t16 CDD cd00051 EFh 530 597 2.08966E-11
22 g11440.t16 Coils Coil Coil 45 72 -
21 g11440.t16 Coils Coil Coil 210 230 -
20 g11440.t16 Coils Coil Coil 494 514 -
13 g11440.t16 Gene3D G3DSA:1.10.418.10 - 1 39 5.2E-8
16 g11440.t16 Gene3D G3DSA:1.20.58.60 - 45 170 2.5E-52
14 g11440.t16 Gene3D G3DSA:1.20.58.60 - 171 282 3.7E-35
17 g11440.t16 Gene3D G3DSA:1.20.58.60 - 283 406 1.7E-49
15 g11440.t16 Gene3D G3DSA:1.20.58.60 - 407 519 1.9E-49
19 g11440.t16 Gene3D G3DSA:1.10.238.10 - 520 602 9.9E-17
18 g11440.t16 Gene3D G3DSA:1.10.238.10 - 604 672 9.0E-31
6 g11440.t16 PANTHER PTHR23167:SF25 ALPHA-ACTININ, SARCOMERIC-LIKE PROTEIN 1 672 0.0
7 g11440.t16 PANTHER PTHR23167 CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED 1 672 0.0
1 g11440.t16 Pfam PF00435 Spectrin repeat 55 162 2.4E-12
3 g11440.t16 Pfam PF00435 Spectrin repeat 174 278 2.8E-23
4 g11440.t16 Pfam PF00435 Spectrin repeat 291 398 1.1E-12
2 g11440.t16 Pfam PF00435 Spectrin repeat 412 512 6.3E-12
5 g11440.t16 Pfam PF08726 Ca2+ insensitive EF hand 602 668 5.8E-28
27 g11440.t16 ProSitePatterns PS00018 EF-hand calcium-binding domain. 539 551 -
36 g11440.t16 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 526 561 11.975
35 g11440.t16 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 567 602 9.715
33 g11440.t16 SMART SM00150 SPEC_4 57 163 1.3
31 g11440.t16 SMART SM00150 SPEC_4 177 278 1.1E-22
32 g11440.t16 SMART SM00150 SPEC_4 292 399 2.8E-4
34 g11440.t16 SMART SM00150 SPEC_4 413 512 0.25
28 g11440.t16 SMART SM00054 efh_1 530 558 0.0038
29 g11440.t16 SMART SM00054 efh_1 571 599 0.38
30 g11440.t16 SMART SM01184 efhand_Ca_insen_2 602 668 2.2E-41
12 g11440.t16 SUPERFAMILY SSF46966 Spectrin repeat 46 169 2.25E-32
9 g11440.t16 SUPERFAMILY SSF46966 Spectrin repeat 170 279 2.09E-24
11 g11440.t16 SUPERFAMILY SSF46966 Spectrin repeat 283 403 1.02E-24
10 g11440.t16 SUPERFAMILY SSF46966 Spectrin repeat 407 519 1.13E-21
8 g11440.t16 SUPERFAMILY SSF47473 EF-hand 520 668 2.9E-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