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.t12 TSS g16754.t12 10830399 10830399
chr_4 g16754 g16754.t12 isoform g16754.t12 10830521 10834929
chr_4 g16754 g16754.t12 exon g16754.t12.exon1 10830521 10830608
chr_4 g16754 g16754.t12 exon g16754.t12.exon2 10830714 10830818
chr_4 g16754 g16754.t12 exon g16754.t12.exon3 10832163 10832285
chr_4 g16754 g16754.t12 exon g16754.t12.exon4 10833177 10833571
chr_4 g16754 g16754.t12 cds g16754.t12.CDS1 10833228 10833571
chr_4 g16754 g16754.t12 exon g16754.t12.exon5 10833816 10833903
chr_4 g16754 g16754.t12 cds g16754.t12.CDS2 10833816 10833903
chr_4 g16754 g16754.t12 exon g16754.t12.exon6 10834010 10834322
chr_4 g16754 g16754.t12 cds g16754.t12.CDS3 10834010 10834322
chr_4 g16754 g16754.t12 exon g16754.t12.exon7 10834387 10834929
chr_4 g16754 g16754.t12 cds g16754.t12.CDS4 10834387 10834496
chr_4 g16754 g16754.t12 TTS g16754.t12 10834937 10834937

Sequences

>g16754.t12 Gene=g16754 Length=1655
ATGAAGACAGTGTCGAGAATTTTCCTTCTACTAAGCGCACTAGCGTTAGTAAGCTGTGAA
GTCTTCTTTGAAGAGAAATTCAGCGATGACTCATGGGAAAAGAAATGGGTTTATTCACAA
CATCCAGGCAAAGAATTTGGTCAGTTTAAGAGAACTGCTGGCAAATTTTTCAATGATGAG
GAAGCTGATAAAGGTCTTCAAACTTCACAAGATGCTCGTTTCTATGCTTTGTCAACTAAA
TTTACACCTTTTAGCAATAAAGATAAACCACTTGTGATACAATTCTCTGTAAAGCATGAG
CAGAACATTGATGTAATGTGGTGGTGGATACCTCAAAATCTTTGACTGCAACCTTGATCA
GAAGGACATGCATGGTGAATCACCATATTTGATCATGTTTGGACCAGATATTTGCGGACC
AGGCACAAAGAAAGTTCATGTTATCTTCAGCTACAAAGGCAAAAATCATTTGATCAAGAA
AGAAATTCGCTGCAAAGATGATGTCTTCACTCACTTTTATACCTTGATTGTTCAACCAGA
TAACACTTATGAAGTTTTGATTGATAATGAGAAAGTTGAATCAGGATCATTGGAAGATGA
TTGGGATTTCTTGCCACCAAAGACAATCAAAGATCCAGAAGCAAAGAAACCAGAAGATTG
GGATGAACGTGCAACCATTCCAGACCCAGATGATAAAAAACCAGAAGATTGGGATCAACC
AGAACACATTCCAGACCCAGATGCCACAAAACCAGAAGATTGGGATGATGAAATTGATGG
AGATTTTGAACCACCAATGATTGACAATCCAGAATACAAAGGTGAATGGAAACCAAAACA
AATTGATAACCCAGCATACAAAGGAATCTGGAAGCATCCAGAAATTGACAATCCAGAATA
TACAGCTGATGCCAATCTTTATCTCCGTGAAGAAGTTTGCGCTGTTGGTCTTGATCTCTG
GCAAGTCAAATCAGGCACAATTTTTGACAATATTTTGTTCACTGATGATGCTGAATATGC
TAAAGAAGCAGCTGCTACATTCAAGGCTACACAAGATGGTGAAAAGAAAATGAAAGATGA
ACAAGATGAAGAAGAAAAGAAGAAGGCTGAAGCTGAAGCAAAAACAGAAGAAAAAGATGA
AGACAATGAAGATTTAGATGATGAAGAAGACAAAGAAGACAGCAAAGGAGAAGCTGAAGC
TGGAGATCATGATGAATTGTAAAAACCTCACCGACGCTAAAAAATTATCCCAAAAAATTT
ATTTTCCTTCCCTTATCATCACATCCAAAACTTTGTTTTCATTTTTGTACTGAATAATTT
CAAAACCGTGTCATTTTGTGCAAAGAATTTCAATTTTTTATGTTTTTATAATTTTGAGAA
ATTTTCATCTCAATTTTGTAGGAATAATTTAAATTATATTAATTTACAAAAGATAAAAAA
TACACAAACTTGAAAGTATAAAACTGTTGATAAGATCCTTCTTTAAAATTTGCTACACAC
ACATAAATAGAAAAATTTCATTAATAATTTAGTTTTAATTTAAGTACATAAAAATAACAA
CTATCAAGTTTGATGTTTTTATTAAAATCAACTTTTTTGTGTGCATGCAGAAGAAAAAAT
TACAATAAATTTTCTTTTAAAAAAAATCAACAAAA

>g16754.t12 Gene=g16754 Length=284
MHGESPYLIMFGPDICGPGTKKVHVIFSYKGKNHLIKKEIRCKDDVFTHFYTLIVQPDNT
YEVLIDNEKVESGSLEDDWDFLPPKTIKDPEAKKPEDWDERATIPDPDDKKPEDWDQPEH
IPDPDATKPEDWDDEIDGDFEPPMIDNPEYKGEWKPKQIDNPAYKGIWKHPEIDNPEYTA
DANLYLREEVCAVGLDLWQVKSGTIFDNILFTDDAEYAKEAAATFKATQDGEKKMKDEQD
EEEKKKAEAEAKTEEKDEDNEDLDDEEDKEDSKGEAEAGDHDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g16754.t12 Coils Coil Coil 232 269 -
13 g16754.t12 Gene3D G3DSA:2.60.120.200 - 1 86 6.1E-31
14 g16754.t12 Gene3D G3DSA:2.10.250.10 Calnexin lumenal domain 87 157 1.8E-31
12 g16754.t12 Gene3D G3DSA:2.60.120.200 - 172 253 8.2E-17
18 g16754.t12 MobiDBLite mobidb-lite consensus disorder prediction 75 132 -
19 g16754.t12 MobiDBLite mobidb-lite consensus disorder prediction 75 127 -
22 g16754.t12 MobiDBLite mobidb-lite consensus disorder prediction 225 284 -
21 g16754.t12 MobiDBLite mobidb-lite consensus disorder prediction 226 253 -
20 g16754.t12 MobiDBLite mobidb-lite consensus disorder prediction 254 273 -
3 g16754.t12 PANTHER PTHR11073 CALRETICULIN AND CALNEXIN 1 281 8.5E-133
4 g16754.t12 PANTHER PTHR11073:SF41 CALRETICULIN 1 281 8.5E-133
8 g16754.t12 PRINTS PR00626 Calreticulin signature 5 21 3.2E-45
7 g16754.t12 PRINTS PR00626 Calreticulin signature 94 107 3.2E-45
9 g16754.t12 PRINTS PR00626 Calreticulin signature 121 143 3.2E-45
5 g16754.t12 PRINTS PR00626 Calreticulin signature 159 178 3.2E-45
6 g16754.t12 PRINTS PR00626 Calreticulin signature 192 212 3.2E-45
1 g16754.t12 Pfam PF00262 Calreticulin family 3 136 1.7E-38
2 g16754.t12 Pfam PF00262 Calreticulin family 138 210 4.4E-23
17 g16754.t12 ProSitePatterns PS00804 Calreticulin family signature 2. 9 17 -
16 g16754.t12 ProSitePatterns PS00805 Calreticulin family repeated motif signature. 121 133 -
10 g16754.t12 SUPERFAMILY SSF49899 Concanavalin A-like lectins/glucanases 1 97 2.37E-31
11 g16754.t12 SUPERFAMILY SSF63887 P-domain of calnexin/calreticulin 80 193 3.14E-45

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

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