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.t17 isoform g11440.t17 16257364 16260310
chr_1 g11440 g11440.t17 exon g11440.t17.exon1 16257364 16258404
chr_1 g11440 g11440.t17 cds g11440.t17.CDS1 16257722 16258404
chr_1 g11440 g11440.t17 exon g11440.t17.exon2 16258475 16259102
chr_1 g11440 g11440.t17 cds g11440.t17.CDS2 16258475 16259102
chr_1 g11440 g11440.t17 exon g11440.t17.exon3 16259168 16259497
chr_1 g11440 g11440.t17 cds g11440.t17.CDS3 16259168 16259497
chr_1 g11440 g11440.t17 exon g11440.t17.exon4 16259567 16260310
chr_1 g11440 g11440.t17 cds g11440.t17.CDS4 16259567 16259725
chr_1 g11440 g11440.t17 TSS g11440.t17 NA NA
chr_1 g11440 g11440.t17 TTS g11440.t17 NA NA

Sequences

>g11440.t17 Gene=g11440 Length=2743
ATGCCTGATGAACGTGCTGTTATGACTTATGTCTCATCTTATTATCATTGCTTTAGTGGC
GCACAAAAGGTAAATGCTTCTTGCTTGACTTGAATCTTTTTCTTTGTTACTTTCATTTAA
TGTTTTTTGTATATAGAATTGTTTCAAGATTATTTTATAATATTAGAATTTTTTTACATT
TTAGGCTGAAACTGCAGCTAACCGTATTTGCAAAGTTTTGAAAGTCAATCAAGAAAATGA
AAGACTTATGGAAGAGTATGAGCGTCTTGCATCTGATGTAAGTATTATAAGGTTTTCATT
ATAAATTCTCATTCATCATTTATTTGTTTATTAGCTTCTTGAATGGATTCGTCGTACAAT
GCCATGGTTAGCATCACGTCATTCCGACAGTACACTAGCTGGCGTTCAAAAGAAACTTGA
AGAGTACCGCACATACAGACGCAAACATAAGCCACCACGTGTCGAGCAAAAAGCAAAATT
GGAAACCAACTTCAATACTCTTCAAACTAAATTACGTCTTTCAAATAGACCCGCTTATAT
GCCAACAGAAGGCAAAATGGTTTCAGATATCGCCAATGCATGGAAAAATTTAGAATTGGC
AGAAAAAGCCTTCGAGGAATGGCTCTTAGCTGAGACTATGCGTCTGGAACGCTTAGAACA
CTTGGCACAAAAGTTTAAGCACAAGGCCGATACACATGAAGAATGGACTCGTGGAAAAGA
AGAAATGCTTCAATCTCAAGATTATCGCAGTTGTCGCTTGTATGAATTGAAGGCTTTGAA
AAAGAAGCACGAAGCATTCGAGTCTGATTTGGCTGCTCATCAAGATCGCGTTGAACAAAT
TGCTGCCATCGCTCAAGAACTCAACACATTGGAATATCACGATTGTGTAACAGTAAATGC
CCGTTGCCAACGCATTTGTGATCAATGGGATCGCTTGGGCGCATTGACACAACGTCGTCG
TCAAGCATTGGATGACTCTGAAAGAGTTCTCGAAAAGATTGATTTGCTTCATTTGGAATT
TGCCAAACGTGCTGCACCATTTAACAATTGGTTAGACGGTGCTCGCGAAGACTTAGTCGA
CATGTTCATTGTTCATACAATGGAAGAAATTCAAGGACTTATCACAGCTCACGATCAATT
CAAAGCTACATTAGGTGAAGCCGATAAGGAATATAATCTCATTGTTGGATTGGTTCGTGA
TGTTGAAGGATTGGTCAATCAATACCAAATTGCAAATGGATTAGAGAATCCATACACTAC
ACTCACCGCTAGAGATTTAACATCAAAATGGGCTGATGTCAAGACATTAGTTCCATCTCG
CGATCAAACTCTTGCCATGGAACTTAAGAAGCAACAAAATAATGAAATGTTACGTCGTCA
ATTTGCTGAAAAGGCAAACAATGTCGGTCCATGGATTGAAAAACAAATGGACGCTGTCAG
CGCTATTGGCATGTCAATCAGTGGATCATTAGAAGAACAATTGCACAGATTGAAGGAATA
TGAACAGGCAGTTTATGCTTACAAACCACATATTGAAGAATTGGAAAAGATTCATCAAGC
AGTACAAGAATCTATGATCTTTGAGAATCGCTACACTAACTACACAATGGAAACATTACG
TGTTGGATGGGAACAGCTTTTAACATCAATTAATAGAAATATCAATGAAGTTGAGAATCA
AATTCTCACACGTGACTCAAAAGGAATCACACAAGAACAGTTGACAGAATTCCGCTCAAG
CTTCAATCACTTTGATAAGAATCGCACTGGTCGCTTAGCTCCAGAAGAATTCAAGTCATG
TTTGGTATCAATTGGATACTCAATTGGAAAGGACAGACAAGGAGAATTAGATTTCCAACG
CATCCTCGCTGTTGTTGATCCAAACAGCACTGGTTATGTACACTTTGACGCTTTTCTTGA
CTTTATGACACGCGAGAGTACCGATACCGACACTGCTGAACAAGTTATTGATTCATTTAG
AATTTTGGCATCTGATAAGCCCTACATTCTTCCTGATGAACTTCGACGTGAATTACCACC
AGATCAAGCTGAATATTGTATCCAAAGAATGCCACCATACAAAGGACCAGGTGCTGTACC
AGGAGCTCTTGATTACATGTCATTCAGTACTGCTCTTTATGGCGAGTCTGATCTGTAAAC
ATACAATGTTCATATTTGAAGTATATCAAATAACACGAGAACTATTTATATAAGCCAAGA
ATATTTTTATATATAACTATCTCGAAGCGAATGTTTGTCTCTTTACTTTTGATCGAAAAT
TTTTGACACATCTCTTTTTGTTTTTAATTTGCATGCGTAAGTGGAAAAAGTTTTCCGCTG
CAACTGAAAAGAAGAAGTAGAAAGAAGCAATCAATTTTTCTATCAGAATGTTCATAATTC
ATTTTAAATTTTTCTTTGTGTTTTTATTGAAAAGAATAATTTTTTCTGCCTTATGTAGTA
ATTTAATGTAATTGAACATCAATCATTAAGAAGCGATATTTTTTATATTTTATTAAACGA
ATGATGATGATGATAATGATAAAAATCATGAAGCAGCTATATTCAAAATTTTATAATAAT
TCGATGTTTCTGCAAAGAAAGAAAAAATAAGCAAAAAATTGTAAAAGGATGAAAAGGAGA
AGTTTTGATTTCACAATATATATTTTATTTATATTTATTATTTTACGAAACATAATGCCA
TGATGAAATAAAATTTAACTTTTAAAAAGAAACTACACTCAAT

>g11440.t17 Gene=g11440 Length=599
MPWLASRHSDSTLAGVQKKLEEYRTYRRKHKPPRVEQKAKLETNFNTLQTKLRLSNRPAY
MPTEGKMVSDIANAWKNLELAEKAFEEWLLAETMRLERLEHLAQKFKHKADTHEEWTRGK
EEMLQSQDYRSCRLYELKALKKKHEAFESDLAAHQDRVEQIAAIAQELNTLEYHDCVTVN
ARCQRICDQWDRLGALTQRRRQALDDSERVLEKIDLLHLEFAKRAAPFNNWLDGAREDLV
DMFIVHTMEEIQGLITAHDQFKATLGEADKEYNLIVGLVRDVEGLVNQYQIANGLENPYT
TLTARDLTSKWADVKTLVPSRDQTLAMELKKQQNNEMLRRQFAEKANNVGPWIEKQMDAV
SAIGMSISGSLEEQLHRLKEYEQAVYAYKPHIEELEKIHQAVQESMIFENRYTNYTMETL
RVGWEQLLTSINRNINEVENQILTRDSKGITQEQLTEFRSSFNHFDKNRTGRLAPEEFKS
CLVSIGYSIGKDRQGELDFQRILAVVDPNSTGYVHFDAFLDFMTRESTDTDTAEQVIDSF
RILASDKPYILPDELRRELPPDQAEYCIQRMPPYKGPGAVPGALDYMSFSTALYGESDL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g11440.t17 CDD cd00176 SPEC 102 329 5.99298E-30
20 g11440.t17 CDD cd00176 SPEC 220 442 3.39271E-14
22 g11440.t17 CDD cd00051 EFh 457 524 2.06834E-11
19 g11440.t17 Coils Coil Coil 137 157 -
18 g11440.t17 Coils Coil Coil 421 441 -
15 g11440.t17 Gene3D G3DSA:1.20.58.60 - 1 97 8.2E-37
13 g11440.t17 Gene3D G3DSA:1.20.58.60 - 98 209 3.1E-35
14 g11440.t17 Gene3D G3DSA:1.20.58.60 - 210 333 1.4E-49
12 g11440.t17 Gene3D G3DSA:1.20.58.60 - 334 446 1.6E-49
16 g11440.t17 Gene3D G3DSA:1.10.238.10 - 447 529 8.4E-17
17 g11440.t17 Gene3D G3DSA:1.10.238.10 - 531 599 7.6E-31
5 g11440.t17 PANTHER PTHR23167:SF25 ALPHA-ACTININ, SARCOMERIC-LIKE PROTEIN 1 599 0.0
6 g11440.t17 PANTHER PTHR23167 CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED 1 599 0.0
3 g11440.t17 Pfam PF00435 Spectrin repeat 101 205 2.4E-23
2 g11440.t17 Pfam PF00435 Spectrin repeat 218 325 9.3E-13
1 g11440.t17 Pfam PF00435 Spectrin repeat 339 439 5.3E-12
4 g11440.t17 Pfam PF08726 Ca2+ insensitive EF hand 529 595 4.9E-28
23 g11440.t17 ProSitePatterns PS00018 EF-hand calcium-binding domain. 466 478 -
30 g11440.t17 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 453 488 11.975
31 g11440.t17 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 494 529 9.715
27 g11440.t17 SMART SM00150 SPEC_4 104 205 1.1E-22
28 g11440.t17 SMART SM00150 SPEC_4 219 326 2.8E-4
29 g11440.t17 SMART SM00150 SPEC_4 340 439 0.25
24 g11440.t17 SMART SM00054 efh_1 457 485 0.0038
25 g11440.t17 SMART SM00054 efh_1 498 526 0.38
26 g11440.t17 SMART SM01184 efhand_Ca_insen_2 529 595 2.2E-41
9 g11440.t17 SUPERFAMILY SSF46966 Spectrin repeat 1 96 4.56E-21
11 g11440.t17 SUPERFAMILY SSF46966 Spectrin repeat 97 206 1.83E-24
10 g11440.t17 SUPERFAMILY SSF46966 Spectrin repeat 210 330 8.51E-25
8 g11440.t17 SUPERFAMILY SSF46966 Spectrin repeat 334 446 9.29E-22
7 g11440.t17 SUPERFAMILY SSF47473 EF-hand 447 595 2.35E-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