Gene loci information

Transcript annotation

  • This transcript has been annotated as Calcium-binding protein E63-1.

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 g10355 g10355.t2 TSS g10355.t2 9060269 9060269
chr_1 g10355 g10355.t2 isoform g10355.t2 9060377 9089750
chr_1 g10355 g10355.t2 exon g10355.t2.exon1 9060377 9060583
chr_1 g10355 g10355.t2 cds g10355.t2.CDS1 9060377 9060583
chr_1 g10355 g10355.t2 exon g10355.t2.exon2 9060681 9060950
chr_1 g10355 g10355.t2 cds g10355.t2.CDS2 9060681 9060950
chr_1 g10355 g10355.t2 exon g10355.t2.exon3 9062953 9062994
chr_1 g10355 g10355.t2 cds g10355.t2.CDS3 9062953 9062994
chr_1 g10355 g10355.t2 exon g10355.t2.exon4 9068805 9068837
chr_1 g10355 g10355.t2 cds g10355.t2.CDS4 9068805 9068837
chr_1 g10355 g10355.t2 exon g10355.t2.exon5 9068931 9068976
chr_1 g10355 g10355.t2 cds g10355.t2.CDS5 9068931 9068976
chr_1 g10355 g10355.t2 exon g10355.t2.exon6 9085522 9085665
chr_1 g10355 g10355.t2 cds g10355.t2.CDS6 9085522 9085665
chr_1 g10355 g10355.t2 exon g10355.t2.exon7 9089106 9089229
chr_1 g10355 g10355.t2 cds g10355.t2.CDS7 9089106 9089229
chr_1 g10355 g10355.t2 exon g10355.t2.exon8 9089428 9089576
chr_1 g10355 g10355.t2 cds g10355.t2.CDS8 9089428 9089576
chr_1 g10355 g10355.t2 exon g10355.t2.exon9 9089634 9089652
chr_1 g10355 g10355.t2 cds g10355.t2.CDS9 9089634 9089652
chr_1 g10355 g10355.t2 exon g10355.t2.exon10 9089714 9089750
chr_1 g10355 g10355.t2 cds g10355.t2.CDS10 9089714 9089750
chr_1 g10355 g10355.t2 TTS g10355.t2 9090432 9090432

Sequences

>g10355.t2 Gene=g10355 Length=1071
ATGGGTGATAATAAATTGAATTCAAATGAGACACAATTATTAAAAGCTATGTATGACAAT
ATTACTCATGGATTAGTTGGATTTTTTGCGGCAGCAATTTTATTTACTGATGACTGGGAT
CGAATGTATTGGGCATTAATATGTATGCTACTTTCATCTTTAATTGATGTTGATCATTTT
ATATCAGCATGGTCTTTAAAATTGGCGAATGCAACAAATCTACATTCTCGACCATTTCTT
CACAATTCAACTATACCATTAGTTCTGATTTTTATCCTCATTTTTTGCCACTTATCATAT
CAAGACAACAACATGATAATGACTCTAACTATTCTAATTGTTGCTTTTACGACACATCAT
TTTCGTGATGCATATCGACGAGGGTTAACATTCTTTTTTTATCAAACATCACCATTACCA
TATTATCTCTACATAGGATTAATTTTAATTACACCTTACTTATTAAAGAGTTTTATTACA
ACGAAGCTGGATACCAAAAAAATAGAAGCTGAGATAAAAGTGCTCGGTCAGACAATTATG
GGGAGAAGAAAAAGTTTACAGCAAAAGCCGACAAATTTTTCAGACGATGAGTTAAAAGAC
TTACGAACGGCTTTTGACTTGCTTGATCGTGACCAAGATGGCATGGTGACACCCACAGAA
CTGCAATTTATGCTCAGAAACTTGGGTATCCATGTGAGCGACGAGTTGATCGATGGTTTA
ATGAAAGAAGCAAGTAAAACTGGAAATGGATTGATAGATGAGACAGAATTCCTACAATGG
ATAGGAAGGATACAAGCATTAAGAGAAGAGTCAACTCCATCTGCCGATGACGATGATCTC
ACACAAGATTTAGTGGCAGCTTTTAGAGTGTTTGACAGAGACAATAATGGTTATATAACA
CGTGATGAACTTCAGCGAGCAATGCAAATGATTGGTGAAAATGTGACTGAAGGACAACTA
AATGACATGCTTGCGCTTGCAGATCTTGACAAAGATGGTAGAATTAATTATGAAGAATTT
GCAAGATTGCTATTAAATAATGAATTACAATGTTTAAATGTTAAAGAATAA

>g10355.t2 Gene=g10355 Length=356
MGDNKLNSNETQLLKAMYDNITHGLVGFFAAAILFTDDWDRMYWALICMLLSSLIDVDHF
ISAWSLKLANATNLHSRPFLHNSTIPLVLIFILIFCHLSYQDNNMIMTLTILIVAFTTHH
FRDAYRRGLTFFFYQTSPLPYYLYIGLILITPYLLKSFITTKLDTKKIEAEIKVLGQTIM
GRRKSLQQKPTNFSDDELKDLRTAFDLLDRDQDGMVTPTELQFMLRNLGIHVSDELIDGL
MKEASKTGNGLIDETEFLQWIGRIQALREESTPSADDDDLTQDLVAAFRVFDRDNNGYIT
RDELQRAMQMIGENVTEGQLNDMLALADLDKDGRINYEEFARLLLNNELQCLNVKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g10355.t2 CDD cd00051 EFh 200 261 7.3839E-12
20 g10355.t2 CDD cd00051 EFh 283 344 1.33432E-20
7 g10355.t2 Gene3D G3DSA:1.10.238.10 - 160 268 1.7E-19
6 g10355.t2 Gene3D G3DSA:1.10.238.10 - 269 354 4.1E-23
3 g10355.t2 PANTHER PTHR23050:SF254 CALCIUM-BINDING PROTEIN E63-1 193 345 1.6E-75
4 g10355.t2 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 193 345 1.6E-75
1 g10355.t2 Pfam PF13499 EF-hand domain pair 199 261 2.2E-12
2 g10355.t2 Pfam PF13499 EF-hand domain pair 284 343 1.8E-14
12 g10355.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 19 -
16 g10355.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 36 -
10 g10355.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 37 42 -
18 g10355.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 43 66 -
13 g10355.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 67 77 -
17 g10355.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 78 98 -
9 g10355.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 99 104 -
15 g10355.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 105 121 -
11 g10355.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 122 140 -
14 g10355.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 141 159 -
8 g10355.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 160 356 -
26 g10355.t2 ProSitePatterns PS00018 EF-hand calcium-binding domain. 209 221 -
25 g10355.t2 ProSitePatterns PS00018 EF-hand calcium-binding domain. 292 304 -
27 g10355.t2 ProSitePatterns PS00018 EF-hand calcium-binding domain. 328 340 -
34 g10355.t2 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 196 231 14.625
32 g10355.t2 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 232 267 8.851
35 g10355.t2 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 279 314 15.518
33 g10355.t2 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 315 350 11.556
31 g10355.t2 SMART SM00054 efh_1 200 228 0.0013
29 g10355.t2 SMART SM00054 efh_1 236 264 3.4
30 g10355.t2 SMART SM00054 efh_1 283 311 1.1E-6
28 g10355.t2 SMART SM00054 efh_1 319 347 0.0074
5 g10355.t2 SUPERFAMILY SSF47473 EF-hand 188 349 3.98E-43
23 g10355.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 35 -
24 g10355.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 42 64 -
21 g10355.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 79 101 -
22 g10355.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 131 153 -

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: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. There were no conditions that were differentially expressed