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.t10 TSS g16754.t10 10830399 10830399
chr_4 g16754 g16754.t10 isoform g16754.t10 10830521 10834496
chr_4 g16754 g16754.t10 exon g16754.t10.exon1 10830521 10830608
chr_4 g16754 g16754.t10 exon g16754.t10.exon2 10830714 10830818
chr_4 g16754 g16754.t10 exon g16754.t10.exon3 10832163 10832285
chr_4 g16754 g16754.t10 exon g16754.t10.exon4 10833177 10833571
chr_4 g16754 g16754.t10 cds g16754.t10.CDS1 10833228 10833571
chr_4 g16754 g16754.t10 exon g16754.t10.exon5 10833816 10833903
chr_4 g16754 g16754.t10 cds g16754.t10.CDS2 10833816 10833903
chr_4 g16754 g16754.t10 exon g16754.t10.exon6 10834010 10834496
chr_4 g16754 g16754.t10 cds g16754.t10.CDS3 10834010 10834348
chr_4 g16754 g16754.t10 TTS g16754.t10 10834937 10834937

Sequences

>g16754.t10 Gene=g16754 Length=1286
ATGAAGACAGTGTCGAGAATTTTCCTTCTACTAAGCGCACTAGCGTTAGTAAGCTGTGAA
GTCTTCTTTGAAGAGAAATTCAGCGATGACTCATGGGAAAAGAAATGGGTTTATTCACAA
CATCCAGGCAAAGAATTTGGTCAGTTTAAGAGAACTGCTGGCAAATTTTTCAATGATGAG
GAAGCTGATAAAGGTCTTCAAACTTCACAAGATGCTCGTTTCTATGCTTTGTCAACTAAA
TTTACACCTTTTAGCAATAAAGATAAACCACTTGTGATACAATTCTCTGTAAAGCATGAG
CAGAACATTGATGTAATGTGGTGGTGGATACCTCAAAATCTTTGACTGCAACCTTGATCA
GAAGGACATGCATGGTGAATCACCATATTTGATCATGTTTGGACCAGATATTTGCGGACC
AGGCACAAAGAAAGTTCATGTTATCTTCAGCTACAAAGGCAAAAATCATTTGATCAAGAA
AGAAATTCGCTGCAAAGATGATGTCTTCACTCACTTTTATACCTTGATTGTTCAACCAGA
TAACACTTATGAAGTTTTGATTGATAATGAGAAAGTTGAATCAGGATCATTGGAAGATGA
TTGGGATTTCTTGCCACCAAAGACAATCAAAGATCCAGAAGCAAAGAAACCAGAAGATTG
GGATGAACGTGCAACCATTCCAGACCCAGATGATAAAAAACCAGAAGATTGGGATCAACC
AGAACACATTCCAGACCCAGATGCCACAAAACCAGAAGATTGGGATGATGAAATTGATGG
AGATTTTGAACCACCAATGATTGACAATCCAGAATACAAAGGTGAATGGAAACCAAAACA
AATTGATAACCCAGCATACAAAGGAATCTGGAAGCATCCAGAAATTGACAATCCAGAATA
TACAGCTGATGCCAATCTTTATCTCCGTGAAGAAGTTTGCGCTGTTGGTCTTGATCTCTG
GCAAGTCAAATCAGGCACAATTTTTGACAATATTTTGTTCACTGATGATGCTGAATATGC
TAAAGAAGCAGCTGCTACATTCAAGGCTACACAAGATGGTGAAAAGAAAATGAAAGATGA
ACAAGATGAAGAAGAAAAGAAGAAGGCTGAAGGTAAAAAATTTGGAACTTTGAATTAATC
TTATGAAATTTATTAAAATATTTTTATTTTTTTTAGCTGAAGCAAAAACAGAAGAAAAAG
ATGAAGACAATGAAGATTTAGATGATGAAGAAGACAAAGAAGACAGCAAAGGAGAAGCTG
AAGCTGGAGATCATGATGAATTGTAA

>g16754.t10 Gene=g16754 Length=256
MHGESPYLIMFGPDICGPGTKKVHVIFSYKGKNHLIKKEIRCKDDVFTHFYTLIVQPDNT
YEVLIDNEKVESGSLEDDWDFLPPKTIKDPEAKKPEDWDERATIPDPDDKKPEDWDQPEH
IPDPDATKPEDWDDEIDGDFEPPMIDNPEYKGEWKPKQIDNPAYKGIWKHPEIDNPEYTA
DANLYLREEVCAVGLDLWQVKSGTIFDNILFTDDAEYAKEAAATFKATQDGEKKMKDEQD
EEEKKKAEGKKFGTLN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g16754.t10 Gene3D G3DSA:2.60.120.200 - 1 86 5.0E-31
20 g16754.t10 Gene3D G3DSA:2.10.250.10 Calnexin lumenal domain 87 157 1.5E-31
19 g16754.t10 Gene3D G3DSA:2.60.120.200 - 171 251 3.5E-17
14 g16754.t10 MobiDBLite mobidb-lite consensus disorder prediction 75 132 -
17 g16754.t10 MobiDBLite mobidb-lite consensus disorder prediction 75 127 -
16 g16754.t10 MobiDBLite mobidb-lite consensus disorder prediction 225 256 -
15 g16754.t10 MobiDBLite mobidb-lite consensus disorder prediction 226 256 -
3 g16754.t10 PANTHER PTHR11073 CALRETICULIN AND CALNEXIN 1 249 1.8E-129
4 g16754.t10 PANTHER PTHR11073:SF41 CALRETICULIN 1 249 1.8E-129
8 g16754.t10 PRINTS PR00626 Calreticulin signature 5 21 2.1E-45
7 g16754.t10 PRINTS PR00626 Calreticulin signature 94 107 2.1E-45
9 g16754.t10 PRINTS PR00626 Calreticulin signature 121 143 2.1E-45
5 g16754.t10 PRINTS PR00626 Calreticulin signature 159 178 2.1E-45
6 g16754.t10 PRINTS PR00626 Calreticulin signature 192 212 2.1E-45
1 g16754.t10 Pfam PF00262 Calreticulin family 3 136 1.4E-38
2 g16754.t10 Pfam PF00262 Calreticulin family 138 210 3.7E-23
13 g16754.t10 ProSitePatterns PS00804 Calreticulin family signature 2. 9 17 -
12 g16754.t10 ProSitePatterns PS00805 Calreticulin family repeated motif signature. 121 133 -
10 g16754.t10 SUPERFAMILY SSF49899 Concanavalin A-like lectins/glucanases 1 97 1.9E-31
11 g16754.t10 SUPERFAMILY SSF63887 P-domain of calnexin/calreticulin 80 193 2.49E-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