Gene loci information

Transcript annotation

  • This transcript has been annotated as Endoplasmic reticulum chaperone BiP.

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_3 g2685 g2685.t4 isoform g2685.t4 19711137 19712123
chr_3 g2685 g2685.t4 exon g2685.t4.exon1 19711137 19711468
chr_3 g2685 g2685.t4 TTS g2685.t4 19711154 19711154
chr_3 g2685 g2685.t4 cds g2685.t4.CDS1 19711459 19711468
chr_3 g2685 g2685.t4 exon g2685.t4.exon2 19711520 19712123
chr_3 g2685 g2685.t4 cds g2685.t4.CDS2 19711520 19712073
chr_3 g2685 g2685.t4 TSS g2685.t4 NA NA

Sequences

>g2685.t4 Gene=g2685 Length=936
GTGATAATCAACATACTGTAACAATTCAAGTTTATGAAGGTGAACGTCCAATGACCAAAG
ACAATCACTTATTAGGTAAATTCGATCTTACTGGCATTCCTCCTGCTCCACGTGGAATCC
CACAAATTGAAGTTTCATTTGAAATCGATGCTAATGGTATTCTTCAAGTATCAGCTGAAG
ATAAGGGCACAGGAAATCGCGAGAAAATTGTAATCACAAATGATCAAAACAGACTCACAC
CAGAAGATATTGAACGTATGATTAAGGATGCTGAGCGTTTTGCTGATGATGACAAGAAAC
TCAAGGAACGTGTCGAGGCACGTAATGAACTTGAGAGTTACGCATACAGTCTGAAAAATC
AAATTGGAGATAAGGAAAAACTTGGAGCAAAATTGTCAGATGATGAAAAGAGCAAAATGG
AAGAGGCTATTGACGAAAAGATCAAATGGTTAGAAGAAAATCAAGATACAGATGCTGAAG
ATTACAAGAAACAAAAGAAAGAACTTGAAGAAGTTGTGCAGCCAATTATCGCTAAATTAT
ATCAAGGACAAGGTGGTGTACCACCACCGACAGGCGATGATGATGATGATCTCAAAGACG
AATTATTTTCCTGAAATCAACCTCAATTTTTTTAATGTTAAATTGTTTATTGTAAAAGCT
ACATTCATTTGTTAATTGAAAGTCATTTTCTCTTTTAATTTTCATTCCGTTCTATATCCG
TTCTCAAAAAAAAATTCTTTTCATAGGTCGCATAAAAAAATACATTTTCCTAGAATTTAA
TTTATTAGTAGAAGAAAAAAGAAATTTACAACCAATGCACATGACTGAATGAGCGAATGC
GTGCGTGATCTTAATTTTGTAATGCATTAGTTTCTATTATGAAACAAATTGAATAAAAAA
CTAAACTAGTAAAACTTAGAAAATAATAGTTCTTTT

>g2685.t4 Gene=g2685 Length=187
MTKDNHLLGKFDLTGIPPAPRGIPQIEVSFEIDANGILQVSAEDKGTGNREKIVITNDQN
RLTPEDIERMIKDAERFADDDKKLKERVEARNELESYAYSLKNQIGDKEKLGAKLSDDEK
SKMEEAIDEKIKWLEENQDTDAEDYKKQKKELEEVVQPIIAKLYQGQGGVPPPTGDDDDD
LKDELFS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2685.t4 Coils Coil Coil 135 155 -
7 g2685.t4 Gene3D G3DSA:2.60.34.10 Substrate Binding Domain Of DNAk; Chain A 1 62 5.2E-25
8 g2685.t4 Gene3D G3DSA:1.20.1270.10 - 63 166 5.6E-36
6 g2685.t4 MobiDBLite mobidb-lite consensus disorder prediction 163 187 -
2 g2685.t4 PANTHER PTHR19375 HEAT SHOCK PROTEIN 70KDA 1 171 3.9E-84
3 g2685.t4 PANTHER PTHR19375:SF380 ENDOPLASMIC RETICULUM CHAPERONE BIP 1 171 3.9E-84
1 g2685.t4 Pfam PF00012 Hsp70 protein 1 165 7.3E-44
5 g2685.t4 SUPERFAMILY SSF100920 Heat shock protein 70kD (HSP70), peptide-binding domain 1 95 1.27E-32
4 g2685.t4 SUPERFAMILY SSF100934 Heat shock protein 70kD (HSP70), C-terminal subdomain 89 171 1.1E-26

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:0005524 ATP binding MF
GO:0016887 ATP hydrolysis activity 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. There were no conditions that were differentially expressed