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.t9 isoform g2685.t9 19711137 19714329
chr_3 g2685 g2685.t9 exon g2685.t9.exon1 19711137 19713361
chr_3 g2685 g2685.t9 TTS g2685.t9 19711154 19711154
chr_3 g2685 g2685.t9 cds g2685.t9.CDS1 19711516 19713361
chr_3 g2685 g2685.t9 exon g2685.t9.exon2 19713517 19713657
chr_3 g2685 g2685.t9 cds g2685.t9.CDS2 19713517 19713644
chr_3 g2685 g2685.t9 exon g2685.t9.exon3 19713964 19714329
chr_3 g2685 g2685.t9 TSS g2685.t9 NA NA

Sequences

>g2685.t9 Gene=g2685 Length=2732
ATGAAAAGTTTGAATGGTTTGAATTTTACATATTACGTTAATTTTTAAATCAAAAATTTT
ATGTCATCCAAAATATGATGAAATATGACCAAGTTTCTCAATAAAACATCCTCTCAAATT
CAAAAATACTCTTTGAAATAGGTTGAAAATGGAACAAAAGAACACGTCAGTATAGAAAAG
AGAGATAGTATAAATTGTGAGCAATGAGACCAAATTTCAAGTCATTTCACTAAAAGGTTT
CACAGAGTAAAGACATCAAAAAAAAGATTGAGTAAAAAATTGAGTTATTTAAAGTGATTT
ATCTAGTGAAGTTAAGTAAATTTAATAATTTTGAATTATCAAATAAGAGTAGTTAAGCTA
TTAAAAAAACAAAATTAAAATGAGATTAACTCTATCATTCGTGGTCGTGGCGGCATTCAG
TGTGCTGGGAGTTCTTTCGAGCGAGGATAAGGATAAAAAAGATATTGGTACAGTGATCGG
TATCGATTTGGGAACGACATATTCATGTGTCGGAGTATATAAGAATGGACGTGTAGAAAT
TATTGCAAATGATCAAGGAAATCGTATCACACCTTCATATGTGGCATTCACTTCTGAAGG
AGAACGATTGATTGGTGATGCAGCTAAAAATCAGCTCACAACAAATCCAGAAAATACTGT
GTTCGATGCTAAACGTCTAATTGGTCGTGAATGGAGTGACTCAGCTGTTCAACATGATAT
CAAATTTTTCCCATTCAAAGTTGTCGAGAAGAACTCAAAGCCACACATTGAAGTGAAAAC
TCAACAAGGCAACAAAGTCTTCACACCTGAAGAAATTTCAGCTATGGTTCTTGGAAAAAT
GAAAGAAACTGCTGAGGCATATTTGGGCAAAAAAGTTACGCACGCTGTTGTCACAGTTCC
AGCTTATTTCAATGATGCTCAACGTCAAGCCACAAAAGATGCTGGTATCATCTCTGGATT
GAATGTTATGCGTATTATTAATGAACCTACTGCAGCAGCTATTGCATATGGGCTTGATAA
AAAAGACGGCGAAAAGAATGTTTTAGTATTCGATCTTGGTGGTGGTACATTCGATGTCTC
GCTTCTTACAATTGATAACGGTGTTTTCGAAGTTGTTGCCACAAATGGTGATACTCACTT
AGGAGGTGAAGATTTTGATCAACGTGTGATGGATCATTTCATTAAATTGTACAAGAAGAA
GAAGGGCAAGGACATTCGTAAAGATAATCGCGCTGTACAGAAACTTCGTCGTGAAGTTGA
AAAGGCTAAACGTGCTCTCTCAGCTAGTCAACAAGTTCGTATTGAAATAGAATCATTCTT
TGAAGGAGAAGACTTTAGCGAATCACTTTCACGTGCCAAATTTGAAGAATTGAATATGGA
TTTGTTCAGATCAACTTTGAAACCAGTTCAAAAAGTCTTGGAAGATGCTGACATGAATAA
GAAAGATGTTGATGAAATTGTTTTGGTCGGTGGTTCAACACGTATTCCAAAAGTTCAGCA
ATTGGTCAAAGAATTCTTCAATGGAAAAGAACCATCACGTGGCATCAATCCAGATGAAGC
TGTTGCTTATGGTGCTGCTGTTCAAGCTGGTGTTCTTTCAGGCGAACAAGACACAGACGC
TATCGTTCTTCTCGATGTCAATCCTTTGACTATGGGTATTGAAACAGTCGGAGGTGTGAT
GACAAAATTGATTCCAAGAAATACAGTTATTCCAACAAAGAAATCTCAAATTTTCTCCAC
TGCCAGTGATAATCAACATACTGTAACAATTCAAGTTTATGAAGGTGAACGTCCAATGAC
CAAAGACAATCACTTATTAGGTAAATTCGATCTTACTGGCATTCCTCCTGCTCCACGTGG
AATCCCACAAATTGAAGTTTCATTTGAAATCGATGCTAATGGTATTCTTCAAGTATCAGC
TGAAGATAAGGGCACAGGAAATCGCGAGAAAATTGTAATCACAAATGATCAAAACAGACT
CACACCAGAAGATATTGAACGTATGATTAAGGATGCTGAGCGTTTTGCTGATGATGACAA
GAAACTCAAGGAACGTGTCGAGGCACGTAATGAACTTGAGAGTTACGCATACAGTCTGAA
AAATCAAATTGGAGATAAGGAAAAACTTGGAGCAAAATTGTCAGATGATGAAAAGAGCAA
AATGGAAGAGGCTATTGACGAAAAGATCAAATGGTTAGAAGAAAATCAAGATACAGATGC
TGAAGATTACAAGAAACAAAAGAAAGAACTTGAAGAAGTTGTGCAGCCAATTATCGCTAA
ATTATATCAAGGACAAGGTGGTGTACCACCACCGACAGGCGATGATGATGATGATCTCAA
AGACGAATTGTAAAAAAGCTCCCAAAAATTCCTTCCCTTCGTACAACATACACAAACAAT
ATTTTCCTGAAATCAACCTCAATTTTTTTAATGTTAAATTGTTTATTGTAAAAGCTACAT
TCATTTGTTAATTGAAAGTCATTTTCTCTTTTAATTTTCATTCCGTTCTATATCCGTTCT
CAAAAAAAAATTCTTTTCATAGGTCGCATAAAAAAATACATTTTCCTAGAATTTAATTTA
TTAGTAGAAGAAAAAAGAAATTTACAACCAATGCACATGACTGAATGAGCGAATGCGTGC
GTGATCTTAATTTTGTAATGCATTAGTTTCTATTATGAAACAAATTGAATAAAAAACTAA
ACTAGTAAAACTTAGAAAATAATAGTTCTTTT

>g2685.t9 Gene=g2685 Length=657
MRLTLSFVVVAAFSVLGVLSSEDKDKKDIGTVIGIDLGTTYSCVGVYKNGRVEIIANDQG
NRITPSYVAFTSEGERLIGDAAKNQLTTNPENTVFDAKRLIGREWSDSAVQHDIKFFPFK
VVEKNSKPHIEVKTQQGNKVFTPEEISAMVLGKMKETAEAYLGKKVTHAVVTVPAYFNDA
QRQATKDAGIISGLNVMRIINEPTAAAIAYGLDKKDGEKNVLVFDLGGGTFDVSLLTIDN
GVFEVVATNGDTHLGGEDFDQRVMDHFIKLYKKKKGKDIRKDNRAVQKLRREVEKAKRAL
SASQQVRIEIESFFEGEDFSESLSRAKFEELNMDLFRSTLKPVQKVLEDADMNKKDVDEI
VLVGGSTRIPKVQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGEQDTDAIVLLDV
NPLTMGIETVGGVMTKLIPRNTVIPTKKSQIFSTASDNQHTVTIQVYEGERPMTKDNHLL
GKFDLTGIPPAPRGIPQIEVSFEIDANGILQVSAEDKGTGNREKIVITNDQNRLTPEDIE
RMIKDAERFADDDKKLKERVEARNELESYAYSLKNQIGDKEKLGAKLSDDEKSKMEEAID
EKIKWLEENQDTDAEDYKKQKKELEEVVQPIIAKLYQGQGGVPPPTGDDDDDLKDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
31 g2685.t9 CDD cd10241 HSPA5-like_NBD 30 404 0.0
25 g2685.t9 Coils Coil Coil 279 306 -
24 g2685.t9 Coils Coil Coil 607 627 -
23 g2685.t9 Coils Coil Coil 650 657 -
20 g2685.t9 Gene3D G3DSA:3.30.420.40 - 32 402 3.2E-178
21 g2685.t9 Gene3D G3DSA:3.30.420.40 - 211 389 3.2E-178
19 g2685.t9 Gene3D G3DSA:3.90.640.10 Actin; Chain A 255 338 3.2E-178
18 g2685.t9 Gene3D G3DSA:2.60.34.10 Substrate Binding Domain Of DNAk; Chain A 403 532 9.4E-59
22 g2685.t9 Gene3D G3DSA:1.20.1270.10 - 534 638 7.0E-35
35 g2685.t9 MobiDBLite mobidb-lite consensus disorder prediction 634 657 -
2 g2685.t9 PANTHER PTHR19375 HEAT SHOCK PROTEIN 70KDA 18 643 0.0
3 g2685.t9 PANTHER PTHR19375:SF380 ENDOPLASMIC RETICULUM CHAPERONE BIP 18 643 0.0
7 g2685.t9 PRINTS PR00301 70kDa heat shock protein signature 31 44 5.9E-83
9 g2685.t9 PRINTS PR00301 70kDa heat shock protein signature 59 71 5.9E-83
11 g2685.t9 PRINTS PR00301 70kDa heat shock protein signature 82 90 5.9E-83
12 g2685.t9 PRINTS PR00301 70kDa heat shock protein signature 169 189 5.9E-83
8 g2685.t9 PRINTS PR00301 70kDa heat shock protein signature 229 239 5.9E-83
4 g2685.t9 PRINTS PR00301 70kDa heat shock protein signature 357 373 5.9E-83
6 g2685.t9 PRINTS PR00301 70kDa heat shock protein signature 389 409 5.9E-83
5 g2685.t9 PRINTS PR00301 70kDa heat shock protein signature 414 433 5.9E-83
10 g2685.t9 PRINTS PR00301 70kDa heat shock protein signature 495 511 5.9E-83
1 g2685.t9 Pfam PF00012 Hsp70 protein 32 637 4.5E-267
27 g2685.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
28 g2685.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
29 g2685.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 16 -
30 g2685.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 20 -
26 g2685.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 657 -
32 g2685.t9 ProSitePatterns PS00297 Heat shock hsp70 proteins family signature 1. 35 42 -
34 g2685.t9 ProSitePatterns PS00329 Heat shock hsp70 proteins family signature 2. 223 236 -
33 g2685.t9 ProSitePatterns PS01036 Heat shock hsp70 proteins family signature 3. 360 374 -
16 g2685.t9 SUPERFAMILY SSF53067 Actin-like ATPase domain 30 214 1.61E-71
15 g2685.t9 SUPERFAMILY SSF53067 Actin-like ATPase domain 216 408 3.27E-67
14 g2685.t9 SUPERFAMILY SSF100920 Heat shock protein 70kD (HSP70), peptide-binding domain 411 567 4.97E-62
13 g2685.t9 SUPERFAMILY SSF100934 Heat shock protein 70kD (HSP70), C-terminal subdomain 561 643 1.11E-25
17 g2685.t9 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -

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