Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t16 isoform g16754.t16 10833813 10834929
chr_4 g16754 g16754.t16 exon g16754.t16.exon1 10833813 10833903
chr_4 g16754 g16754.t16 cds g16754.t16.CDS1 10833901 10833903
chr_4 g16754 g16754.t16 exon g16754.t16.exon2 10834010 10834322
chr_4 g16754 g16754.t16 cds g16754.t16.CDS2 10834010 10834322
chr_4 g16754 g16754.t16 exon g16754.t16.exon3 10834387 10834929
chr_4 g16754 g16754.t16 cds g16754.t16.CDS3 10834387 10834496
chr_4 g16754 g16754.t16 TTS g16754.t16 10834937 10834937
chr_4 g16754 g16754.t16 TSS g16754.t16 NA NA

Sequences

>g16754.t16 Gene=g16754 Length=947
TAGGGATCAACCAGAACACATTCCAGACCCAGATGCCACAAAACCAGAAGATTGGGATGA
TGAAATTGATGGAGATTTTGAACCACCAATGATTGACAATCCAGAATACAAAGGTGAATG
GAAACCAAAACAAATTGATAACCCAGCATACAAAGGAATCTGGAAGCATCCAGAAATTGA
CAATCCAGAATATACAGCTGATGCCAATCTTTATCTCCGTGAAGAAGTTTGCGCTGTTGG
TCTTGATCTCTGGCAAGTCAAATCAGGCACAATTTTTGACAATATTTTGTTCACTGATGA
TGCTGAATATGCTAAAGAAGCAGCTGCTACATTCAAGGCTACACAAGATGGTGAAAAGAA
AATGAAAGATGAACAAGATGAAGAAGAAAAGAAGAAGGCTGAAGCTGAAGCAAAAACAGA
AGAAAAAGATGAAGACAATGAAGATTTAGATGATGAAGAAGACAAAGAAGACAGCAAAGG
AGAAGCTGAAGCTGGAGATCATGATGAATTGTAAAAACCTCACCGACGCTAAAAAATTAT
CCCAAAAAATTTATTTTCCTTCCCTTATCATCACATCCAAAACTTTGTTTTCATTTTTGT
ACTGAATAATTTCAAAACCGTGTCATTTTGTGCAAAGAATTTCAATTTTTTATGTTTTTA
TAATTTTGAGAAATTTTCATCTCAATTTTGTAGGAATAATTTAAATTATATTAATTTACA
AAAGATAAAAAATACACAAACTTGAAAGTATAAAACTGTTGATAAGATCCTTCTTTAAAA
TTTGCTACACACACATAAATAGAAAAATTTCATTAATAATTTAGTTTTAATTTAAGTACA
TAAAAATAACAACTATCAAGTTTGATGTTTTTATTAAAATCAACTTTTTTGTGTGCATGC
AGAAGAAAAAATTACAATAAATTTTCTTTTAAAAAAAATCAACAAAA

>g16754.t16 Gene=g16754 Length=141
MIDNPEYKGEWKPKQIDNPAYKGIWKHPEIDNPEYTADANLYLREEVCAVGLDLWQVKSG
TIFDNILFTDDAEYAKEAAATFKATQDGEKKMKDEQDEEEKKKAEAEAKTEEKDEDNEDL
DDEEDKEDSKGEAEAGDHDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g16754.t16 Coils Coil Coil 89 126 -
11 g16754.t16 Gene3D G3DSA:2.10.250.10 Calnexin lumenal domain 1 42 4.6E-26
10 g16754.t16 Gene3D G3DSA:2.60.120.200 - 43 77 4.6E-26
8 g16754.t16 MobiDBLite mobidb-lite consensus disorder prediction 82 141 -
7 g16754.t16 MobiDBLite mobidb-lite consensus disorder prediction 83 110 -
9 g16754.t16 MobiDBLite mobidb-lite consensus disorder prediction 111 130 -
2 g16754.t16 PANTHER PTHR11073:SF42 CALR PROTEIN 1 139 3.4E-46
3 g16754.t16 PANTHER PTHR11073 CALRETICULIN AND CALNEXIN 1 139 3.4E-46
4 g16754.t16 PRINTS PR00626 Calreticulin signature 16 35 1.3E-16
5 g16754.t16 PRINTS PR00626 Calreticulin signature 49 69 1.3E-16
1 g16754.t16 Pfam PF00262 Calreticulin family 1 67 4.0E-21
6 g16754.t16 SUPERFAMILY SSF63887 P-domain of calnexin/calreticulin 1 50 5.23E-17

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