Gene loci information

Transcript annotation

  • This transcript has been annotated as Calreticulin.

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_4 g16754 g16754.t11 TSS g16754.t11 10830399 10830399
chr_4 g16754 g16754.t11 isoform g16754.t11 10830521 10834929
chr_4 g16754 g16754.t11 exon g16754.t11.exon1 10830521 10830608
chr_4 g16754 g16754.t11 cds g16754.t11.CDS1 10830521 10830608
chr_4 g16754 g16754.t11 exon g16754.t11.exon2 10830714 10830818
chr_4 g16754 g16754.t11 cds g16754.t11.CDS2 10830714 10830818
chr_4 g16754 g16754.t11 exon g16754.t11.exon3 10832163 10832281
chr_4 g16754 g16754.t11 cds g16754.t11.CDS3 10832163 10832281
chr_4 g16754 g16754.t11 exon g16754.t11.exon4 10833177 10833571
chr_4 g16754 g16754.t11 cds g16754.t11.CDS4 10833177 10833571
chr_4 g16754 g16754.t11 exon g16754.t11.exon5 10833816 10833903
chr_4 g16754 g16754.t11 cds g16754.t11.CDS5 10833816 10833903
chr_4 g16754 g16754.t11 exon g16754.t11.exon6 10834010 10834322
chr_4 g16754 g16754.t11 cds g16754.t11.CDS6 10834010 10834322
chr_4 g16754 g16754.t11 exon g16754.t11.exon7 10834402 10834929
chr_4 g16754 g16754.t11 cds g16754.t11.CDS7 10834402 10834496
chr_4 g16754 g16754.t11 TTS g16754.t11 10834937 10834937

Sequences

>g16754.t11 Gene=g16754 Length=1636
ATGAAGACAGTGTCGAGAATTTTCCTTCTACTAAGCGCACTAGCGTTAGTAAGCTGTGAA
GTCTTCTTTGAAGAGAAATTCAGCGATGACTCATGGGAAAAGAAATGGGTTTATTCACAA
CATCCAGGCAAAGAATTTGGTCAGTTTAAGAGAACTGCTGGCAAATTTTTCAATGATGAG
GAAGCTGATAAAGGTCTTCAAACTTCACAAGATGCTCGTTTCTATGCTTTGTCAACTAAA
TTTACACCTTTTAGCAATAAAGATAAACCACTTGTGATACAATTCTCTGTAAAGCATGAG
CAGAACATTGATTGTGGTGGTGGATACCTCAAAATCTTTGACTGCAACCTTGATCAGAAG
GACATGCATGGTGAATCACCATATTTGATCATGTTTGGACCAGATATTTGCGGACCAGGC
ACAAAGAAAGTTCATGTTATCTTCAGCTACAAAGGCAAAAATCATTTGATCAAGAAAGAA
ATTCGCTGCAAAGATGATGTCTTCACTCACTTTTATACCTTGATTGTTCAACCAGATAAC
ACTTATGAAGTTTTGATTGATAATGAGAAAGTTGAATCAGGATCATTGGAAGATGATTGG
GATTTCTTGCCACCAAAGACAATCAAAGATCCAGAAGCAAAGAAACCAGAAGATTGGGAT
GAACGTGCAACCATTCCAGACCCAGATGATAAAAAACCAGAAGATTGGGATCAACCAGAA
CACATTCCAGACCCAGATGCCACAAAACCAGAAGATTGGGATGATGAAATTGATGGAGAT
TTTGAACCACCAATGATTGACAATCCAGAATACAAAGGTGAATGGAAACCAAAACAAATT
GATAACCCAGCATACAAAGGAATCTGGAAGCATCCAGAAATTGACAATCCAGAATATACA
GCTGATGCCAATCTTTATCTCCGTGAAGAAGTTTGCGCTGTTGGTCTTGATCTCTGGCAA
GTCAAATCAGGCACAATTTTTGACAATATTTTGTTCACTGATGATGCTGAATATGCTAAA
GAAGCAGCTGCTACATTCAAGGCTACACAAGATGGTGAAAAGAAAATGAAAGATGAACAA
GATGAAGAAGAAAAGAAGAAGGCTGAAGAAGAAAAAGATGAAGACAATGAAGATTTAGAT
GATGAAGAAGACAAAGAAGACAGCAAAGGAGAAGCTGAAGCTGGAGATCATGATGAATTG
TAAAAACCTCACCGACGCTAAAAAATTATCCCAAAAAATTTATTTTCCTTCCCTTATCAT
CACATCCAAAACTTTGTTTTCATTTTTGTACTGAATAATTTCAAAACCGTGTCATTTTGT
GCAAAGAATTTCAATTTTTTATGTTTTTATAATTTTGAGAAATTTTCATCTCAATTTTGT
AGGAATAATTTAAATTATATTAATTTACAAAAGATAAAAAATACACAAACTTGAAAGTAT
AAAACTGTTGATAAGATCCTTCTTTAAAATTTGCTACACACACATAAATAGAAAAATTTC
ATTAATAATTTAGTTTTAATTTAAGTACATAAAAATAACAACTATCAAGTTTGATGTTTT
TATTAAAATCAACTTTTTTGTGTGCATGCAGAAGAAAAAATTACAATAAATTTTCTTTTA
AAAAAAATCAACAAAA

>g16754.t11 Gene=g16754 Length=400
MKTVSRIFLLLSALALVSCEVFFEEKFSDDSWEKKWVYSQHPGKEFGQFKRTAGKFFNDE
EADKGLQTSQDARFYALSTKFTPFSNKDKPLVIQFSVKHEQNIDCGGGYLKIFDCNLDQK
DMHGESPYLIMFGPDICGPGTKKVHVIFSYKGKNHLIKKEIRCKDDVFTHFYTLIVQPDN
TYEVLIDNEKVESGSLEDDWDFLPPKTIKDPEAKKPEDWDERATIPDPDDKKPEDWDQPE
HIPDPDATKPEDWDDEIDGDFEPPMIDNPEYKGEWKPKQIDNPAYKGIWKHPEIDNPEYT
ADANLYLREEVCAVGLDLWQVKSGTIFDNILFTDDAEYAKEAAATFKATQDGEKKMKDEQ
DEEEKKKAEEEKDEDNEDLDDEEDKEDSKGEAEAGDHDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g16754.t11 Coils Coil Coil 353 385 -
15 g16754.t11 Gene3D G3DSA:2.60.120.200 - 12 224 1.3E-80
17 g16754.t11 Gene3D G3DSA:2.10.250.10 Calnexin lumenal domain 225 286 2.6E-23
16 g16754.t11 Gene3D G3DSA:2.60.120.200 - 293 373 1.7E-16
31 g16754.t11 MobiDBLite mobidb-lite consensus disorder prediction 196 248 -
32 g16754.t11 MobiDBLite mobidb-lite consensus disorder prediction 196 253 -
33 g16754.t11 MobiDBLite mobidb-lite consensus disorder prediction 346 400 -
30 g16754.t11 MobiDBLite mobidb-lite consensus disorder prediction 347 372 -
29 g16754.t11 MobiDBLite mobidb-lite consensus disorder prediction 373 389 -
3 g16754.t11 PANTHER PTHR11073 CALRETICULIN AND CALNEXIN 1 396 6.8E-185
4 g16754.t11 PANTHER PTHR11073:SF41 CALRETICULIN 1 396 6.8E-185
24 g16754.t11 PIRSF PIRSF002356 Calreticulin 1 400 1.1E-195
7 g16754.t11 PRINTS PR00626 Calreticulin signature 100 118 1.9E-53
6 g16754.t11 PRINTS PR00626 Calreticulin signature 126 142 1.9E-53
8 g16754.t11 PRINTS PR00626 Calreticulin signature 215 228 1.9E-53
10 g16754.t11 PRINTS PR00626 Calreticulin signature 242 264 1.9E-53
5 g16754.t11 PRINTS PR00626 Calreticulin signature 280 299 1.9E-53
9 g16754.t11 PRINTS PR00626 Calreticulin signature 313 333 1.9E-53
1 g16754.t11 Pfam PF00262 Calreticulin family 23 257 2.5E-59
2 g16754.t11 Pfam PF00262 Calreticulin family 259 331 7.4E-23
20 g16754.t11 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
21 g16754.t11 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
22 g16754.t11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 14 -
23 g16754.t11 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
19 g16754.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 400 -
26 g16754.t11 ProSitePatterns PS00803 Calreticulin family signature 1. 98 113 -
28 g16754.t11 ProSitePatterns PS00804 Calreticulin family signature 2. 130 138 -
27 g16754.t11 ProSitePatterns PS00805 Calreticulin family repeated motif signature. 242 254 -
34 g16754.t11 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 19 6.0
11 g16754.t11 SUPERFAMILY SSF49899 Concanavalin A-like lectins/glucanases 16 218 2.69E-61
12 g16754.t11 SUPERFAMILY SSF63887 P-domain of calnexin/calreticulin 201 314 6.28E-45
14 g16754.t11 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
25 g16754.t11 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 23 -
13 g16754.t11 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 23 -

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:0006457 protein folding BP
GO:0005783 endoplasmic reticulum CC
GO:0005515 protein binding MF
GO:0051082 unfolded 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