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.t1 TTS g2685.t1 19711154 19711154
chr_3 g2685 g2685.t1 isoform g2685.t1 19711516 19714329
chr_3 g2685 g2685.t1 exon g2685.t1.exon1 19711516 19713361
chr_3 g2685 g2685.t1 cds g2685.t1.CDS1 19711516 19713361
chr_3 g2685 g2685.t1 exon g2685.t1.exon2 19713517 19713661
chr_3 g2685 g2685.t1 cds g2685.t1.CDS2 19713517 19713661
chr_3 g2685 g2685.t1 exon g2685.t1.exon3 19713964 19713972
chr_3 g2685 g2685.t1 cds g2685.t1.CDS3 19713964 19713972
chr_3 g2685 g2685.t1 exon g2685.t1.exon4 19714314 19714329
chr_3 g2685 g2685.t1 cds g2685.t1.CDS4 19714314 19714329
chr_3 g2685 g2685.t1 TSS g2685.t1 NA NA

Sequences

>g2685.t1 Gene=g2685 Length=2016
ATGAAAAGTTTGAATGCTATTAAAAGTAGAAACAAAATTAAAATGAGATTAACTCTATCA
TTCGTGGTCGTGGCGGCATTCAGTGTGCTGGGAGTTCTTTCGAGCGAGGATAAGGATAAA
AAAGATATTGGTACAGTGATCGGTATCGATTTGGGAACGACATATTCATGTGTCGGAGTA
TATAAGAATGGACGTGTAGAAATTATTGCAAATGATCAAGGAAATCGTATCACACCTTCA
TATGTGGCATTCACTTCTGAAGGAGAACGATTGATTGGTGATGCAGCTAAAAATCAGCTC
ACAACAAATCCAGAAAATACTGTGTTCGATGCTAAACGTCTAATTGGTCGTGAATGGAGT
GACTCAGCTGTTCAACATGATATCAAATTTTTCCCATTCAAAGTTGTCGAGAAGAACTCA
AAGCCACACATTGAAGTGAAAACTCAACAAGGCAACAAAGTCTTCACACCTGAAGAAATT
TCAGCTATGGTTCTTGGAAAAATGAAAGAAACTGCTGAGGCATATTTGGGCAAAAAAGTT
ACGCACGCTGTTGTCACAGTTCCAGCTTATTTCAATGATGCTCAACGTCAAGCCACAAAA
GATGCTGGTATCATCTCTGGATTGAATGTTATGCGTATTATTAATGAACCTACTGCAGCA
GCTATTGCATATGGGCTTGATAAAAAAGACGGCGAAAAGAATGTTTTAGTATTCGATCTT
GGTGGTGGTACATTCGATGTCTCGCTTCTTACAATTGATAACGGTGTTTTCGAAGTTGTT
GCCACAAATGGTGATACTCACTTAGGAGGTGAAGATTTTGATCAACGTGTGATGGATCAT
TTCATTAAATTGTACAAGAAGAAGAAGGGCAAGGACATTCGTAAAGATAATCGCGCTGTA
CAGAAACTTCGTCGTGAAGTTGAAAAGGCTAAACGTGCTCTCTCAGCTAGTCAACAAGTT
CGTATTGAAATAGAATCATTCTTTGAAGGAGAAGACTTTAGCGAATCACTTTCACGTGCC
AAATTTGAAGAATTGAATATGGATTTGTTCAGATCAACTTTGAAACCAGTTCAAAAAGTC
TTGGAAGATGCTGACATGAATAAGAAAGATGTTGATGAAATTGTTTTGGTCGGTGGTTCA
ACACGTATTCCAAAAGTTCAGCAATTGGTCAAAGAATTCTTCAATGGAAAAGAACCATCA
CGTGGCATCAATCCAGATGAAGCTGTTGCTTATGGTGCTGCTGTTCAAGCTGGTGTTCTT
TCAGGCGAACAAGACACAGACGCTATCGTTCTTCTCGATGTCAATCCTTTGACTATGGGT
ATTGAAACAGTCGGAGGTGTGATGACAAAATTGATTCCAAGAAATACAGTTATTCCAACA
AAGAAATCTCAAATTTTCTCCACTGCCAGTGATAATCAACATACTGTAACAATTCAAGTT
TATGAAGGTGAACGTCCAATGACCAAAGACAATCACTTATTAGGTAAATTCGATCTTACT
GGCATTCCTCCTGCTCCACGTGGAATCCCACAAATTGAAGTTTCATTTGAAATCGATGCT
AATGGTATTCTTCAAGTATCAGCTGAAGATAAGGGCACAGGAAATCGCGAGAAAATTGTA
ATCACAAATGATCAAAACAGACTCACACCAGAAGATATTGAACGTATGATTAAGGATGCT
GAGCGTTTTGCTGATGATGACAAGAAACTCAAGGAACGTGTCGAGGCACGTAATGAACTT
GAGAGTTACGCATACAGTCTGAAAAATCAAATTGGAGATAAGGAAAAACTTGGAGCAAAA
TTGTCAGATGATGAAAAGAGCAAAATGGAAGAGGCTATTGACGAAAAGATCAAATGGTTA
GAAGAAAATCAAGATACAGATGCTGAAGATTACAAGAAACAAAAGAAAGAACTTGAAGAA
GTTGTGCAGCCAATTATCGCTAAATTATATCAAGGACAAGGTGGTGTACCACCACCGACA
GGCGATGATGATGATGATCTCAAAGACGAATTGTAA

>g2685.t1 Gene=g2685 Length=671
MKSLNAIKSRNKIKMRLTLSFVVVAAFSVLGVLSSEDKDKKDIGTVIGIDLGTTYSCVGV
YKNGRVEIIANDQGNRITPSYVAFTSEGERLIGDAAKNQLTTNPENTVFDAKRLIGREWS
DSAVQHDIKFFPFKVVEKNSKPHIEVKTQQGNKVFTPEEISAMVLGKMKETAEAYLGKKV
THAVVTVPAYFNDAQRQATKDAGIISGLNVMRIINEPTAAAIAYGLDKKDGEKNVLVFDL
GGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMDHFIKLYKKKKGKDIRKDNRAV
QKLRREVEKAKRALSASQQVRIEIESFFEGEDFSESLSRAKFEELNMDLFRSTLKPVQKV
LEDADMNKKDVDEIVLVGGSTRIPKVQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVL
SGEQDTDAIVLLDVNPLTMGIETVGGVMTKLIPRNTVIPTKKSQIFSTASDNQHTVTIQV
YEGERPMTKDNHLLGKFDLTGIPPAPRGIPQIEVSFEIDANGILQVSAEDKGTGNREKIV
ITNDQNRLTPEDIERMIKDAERFADDDKKLKERVEARNELESYAYSLKNQIGDKEKLGAK
LSDDEKSKMEEAIDEKIKWLEENQDTDAEDYKKQKKELEEVVQPIIAKLYQGQGGVPPPT
GDDDDDLKDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
30 g2685.t1 CDD cd10241 HSPA5-like_NBD 44 418 0.0
24 g2685.t1 Coils Coil Coil 293 320 -
23 g2685.t1 Coils Coil Coil 621 641 -
20 g2685.t1 Gene3D G3DSA:3.30.420.40 - 46 416 3.4E-178
21 g2685.t1 Gene3D G3DSA:3.30.420.40 - 225 403 3.4E-178
19 g2685.t1 Gene3D G3DSA:3.90.640.10 Actin; Chain A 269 352 3.4E-178
18 g2685.t1 Gene3D G3DSA:2.60.34.10 Substrate Binding Domain Of DNAk; Chain A 417 546 9.7E-59
22 g2685.t1 Gene3D G3DSA:1.20.1270.10 - 548 652 7.2E-35
35 g2685.t1 MobiDBLite mobidb-lite consensus disorder prediction 648 671 -
2 g2685.t1 PANTHER PTHR19375 HEAT SHOCK PROTEIN 70KDA 32 657 0.0
3 g2685.t1 PANTHER PTHR19375:SF380 ENDOPLASMIC RETICULUM CHAPERONE BIP 32 657 0.0
8 g2685.t1 PRINTS PR00301 70kDa heat shock protein signature 45 58 7.0E-83
5 g2685.t1 PRINTS PR00301 70kDa heat shock protein signature 73 85 7.0E-83
12 g2685.t1 PRINTS PR00301 70kDa heat shock protein signature 96 104 7.0E-83
6 g2685.t1 PRINTS PR00301 70kDa heat shock protein signature 183 203 7.0E-83
4 g2685.t1 PRINTS PR00301 70kDa heat shock protein signature 243 253 7.0E-83
11 g2685.t1 PRINTS PR00301 70kDa heat shock protein signature 371 387 7.0E-83
9 g2685.t1 PRINTS PR00301 70kDa heat shock protein signature 403 423 7.0E-83
10 g2685.t1 PRINTS PR00301 70kDa heat shock protein signature 428 447 7.0E-83
7 g2685.t1 PRINTS PR00301 70kDa heat shock protein signature 509 525 7.0E-83
1 g2685.t1 Pfam PF00012 Hsp70 protein 46 651 4.9E-267
26 g2685.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 34 -
27 g2685.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 16 -
28 g2685.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 17 30 -
29 g2685.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 31 34 -
25 g2685.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 35 671 -
32 g2685.t1 ProSitePatterns PS00297 Heat shock hsp70 proteins family signature 1. 49 56 -
34 g2685.t1 ProSitePatterns PS00329 Heat shock hsp70 proteins family signature 2. 237 250 -
33 g2685.t1 ProSitePatterns PS01036 Heat shock hsp70 proteins family signature 3. 374 388 -
16 g2685.t1 SUPERFAMILY SSF53067 Actin-like ATPase domain 44 228 1.68E-71
15 g2685.t1 SUPERFAMILY SSF53067 Actin-like ATPase domain 230 422 3.46E-67
14 g2685.t1 SUPERFAMILY SSF100920 Heat shock protein 70kD (HSP70), peptide-binding domain 425 581 5.1E-62
13 g2685.t1 SUPERFAMILY SSF100934 Heat shock protein 70kD (HSP70), C-terminal subdomain 575 657 1.15E-25
17 g2685.t1 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 35 -
31 g2685.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -

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

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