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.t10 isoform g2685.t10 19711137 19714329
chr_3 g2685 g2685.t10 exon g2685.t10.exon1 19711137 19712162
chr_3 g2685 g2685.t10 TTS g2685.t10 19711154 19711154
chr_3 g2685 g2685.t10 cds g2685.t10.CDS1 19711516 19712162
chr_3 g2685 g2685.t10 exon g2685.t10.exon2 19712400 19713361
chr_3 g2685 g2685.t10 cds g2685.t10.CDS2 19712400 19713361
chr_3 g2685 g2685.t10 exon g2685.t10.exon3 19713517 19713661
chr_3 g2685 g2685.t10 cds g2685.t10.CDS3 19713517 19713644
chr_3 g2685 g2685.t10 exon g2685.t10.exon4 19713964 19714329
chr_3 g2685 g2685.t10 TSS g2685.t10 NA NA

Sequences

>g2685.t10 Gene=g2685 Length=2499
ATGAAAAGTTTGAATGGTTTGAATTTTACATATTACGTTAATTTTTAAATCAAAAATTTT
ATGTCATCCAAAATATGATGAAATATGACCAAGTTTCTCAATAAAACATCCTCTCAAATT
CAAAAATACTCTTTGAAATAGGTTGAAAATGGAACAAAAGAACACGTCAGTATAGAAAAG
AGAGATAGTATAAATTGTGAGCAATGAGACCAAATTTCAAGTCATTTCACTAAAAGGTTT
CACAGAGTAAAGACATCAAAAAAAAGATTGAGTAAAAAATTGAGTTATTTAAAGTGATTT
ATCTAGTGAAGTTAAGTAAATTTAATAATTTTGAATTATCAAATAAGAGTAGTTAAGCTA
TTAAAAGTAGAAACAAAATTAAAATGAGATTAACTCTATCATTCGTGGTCGTGGCGGCAT
TCAGTGTGCTGGGAGTTCTTTCGAGCGAGGATAAGGATAAAAAAGATATTGGTACAGTGA
TCGGTATCGATTTGGGAACGACATATTCATGTGTCGGAGTATATAAGAATGGACGTGTAG
AAATTATTGCAAATGATCAAGGAAATCGTATCACACCTTCATATGTGGCATTCACTTCTG
AAGGAGAACGATTGATTGGTGATGCAGCTAAAAATCAGCTCACAACAAATCCAGAAAATA
CTGTGTTCGATGCTAAACGTCTAATTGGTCGTGAATGGAGTGACTCAGCTGTTCAACATG
ATATCAAATTTTTCCCATTCAAAGTTGTCGAGAAGAACTCAAAGCCACACATTGAAGTGA
AAACTCAACAAGGCAACAAAGTCTTCACACCTGAAGAAATTTCAGCTATGGTTCTTGGAA
AAATGAAAGAAACTGCTGAGGCATATTTGGGCAAAAAAGTTACGCACGCTGTTGTCACAG
TTCCAGCTTATTTCAATGATGCTCAACGTCAAGCCACAAAAGATGCTGGTATCATCTCTG
GATTGAATGTTATGCGTATTATTAATGAACCTACTGCAGCAGCTATTGCATATGGGCTTG
ATAAAAAAGACGGCGAAAAGAATGTTTTAGTATTCGATCTTGGTGGTGGTACATTCGATG
TCTCGCTTCTTACAATTGATAACGGTGTTTTCGAAGTTGTTGCCACAAATGGTGATACTC
ACTTAGGAGGTGAAGATTTTGATCAACGTGTGATGGATCATTTCATTAAATTGTACAAGA
AGAAGAAGGGCAAGGACATTCGTAAAGATAATCGCGCTGTACAGAAACTTCGTCGTGAAG
TTGAAAAGGCTAAACGTGCTCTCTCAGCTAGTCAACAAGTTCGTATTGAAATAGAATCAT
TCTTTGAAGGAGAAGACTTTAGCGAATCACTTTCACGTGCCAAATTTGAAGAATTGAATA
TGGATTTGTTCAGATCAACTTTGAAACCAGTTCAAAAAGTCTTGGAAGATGCTGACATGA
ATAAGAAAGATGTTGATGAAATTGTTTTGGTCGTTATTCCAACAAAGAAATCTCAAATTT
TCTCCACTGCCAGTGATAATCAACATACTGTAACAATTCAAGTTTATGAAGGTGAACGTC
CAATGACCAAAGACAATCACTTATTAGGTAAATTCGATCTTACTGGCATTCCTCCTGCTC
CACGTGGAATCCCACAAATTGAAGTTTCATTTGAAATCGATGCTAATGGTATTCTTCAAG
TATCAGCTGAAGATAAGGGCACAGGAAATCGCGAGAAAATTGTAATCACAAATGATCAAA
ACAGACTCACACCAGAAGATATTGAACGTATGATTAAGGATGCTGAGCGTTTTGCTGATG
ATGACAAGAAACTCAAGGAACGTGTCGAGGCACGTAATGAACTTGAGAGTTACGCATACA
GTCTGAAAAATCAAATTGGAGATAAGGAAAAACTTGGAGCAAAATTGTCAGATGATGAAA
AGAGCAAAATGGAAGAGGCTATTGACGAAAAGATCAAATGGTTAGAAGAAAATCAAGATA
CAGATGCTGAAGATTACAAGAAACAAAAGAAAGAACTTGAAGAAGTTGTGCAGCCAATTA
TCGCTAAATTATATCAAGGACAAGGTGGTGTACCACCACCGACAGGCGATGATGATGATG
ATCTCAAAGACGAATTGTAAAAAAGCTCCCAAAAATTCCTTCCCTTCGTACAACATACAC
AAACAATATTTTCCTGAAATCAACCTCAATTTTTTTAATGTTAAATTGTTTATTGTAAAA
GCTACATTCATTTGTTAATTGAAAGTCATTTTCTCTTTTAATTTTCATTCCGTTCTATAT
CCGTTCTCAAAAAAAAATTCTTTTCATAGGTCGCATAAAAAAATACATTTTCCTAGAATT
TAATTTATTAGTAGAAGAAAAAAGAAATTTACAACCAATGCACATGACTGAATGAGCGAA
TGCGTGCGTGATCTTAATTTTGTAATGCATTAGTTTCTATTATGAAACAAATTGAATAAA
AAACTAAACTAGTAAAACTTAGAAAATAATAGTTCTTTT

>g2685.t10 Gene=g2685 Length=578
MRLTLSFVVVAAFSVLGVLSSEDKDKKDIGTVIGIDLGTTYSCVGVYKNGRVEIIANDQG
NRITPSYVAFTSEGERLIGDAAKNQLTTNPENTVFDAKRLIGREWSDSAVQHDIKFFPFK
VVEKNSKPHIEVKTQQGNKVFTPEEISAMVLGKMKETAEAYLGKKVTHAVVTVPAYFNDA
QRQATKDAGIISGLNVMRIINEPTAAAIAYGLDKKDGEKNVLVFDLGGGTFDVSLLTIDN
GVFEVVATNGDTHLGGEDFDQRVMDHFIKLYKKKKGKDIRKDNRAVQKLRREVEKAKRAL
SASQQVRIEIESFFEGEDFSESLSRAKFEELNMDLFRSTLKPVQKVLEDADMNKKDVDEI
VLVVIPTKKSQIFSTASDNQHTVTIQVYEGERPMTKDNHLLGKFDLTGIPPAPRGIPQIE
VSFEIDANGILQVSAEDKGTGNREKIVITNDQNRLTPEDIERMIKDAERFADDDKKLKER
VEARNELESYAYSLKNQIGDKEKLGAKLSDDEKSKMEEAIDEKIKWLEENQDTDAEDYKK
QKKELEEVVQPIIAKLYQGQGGVPPPTGDDDDDLKDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
30 g2685.t10 CDD cd10241 HSPA5-like_NBD 30 363 0.0
24 g2685.t10 Coils Coil Coil 279 306 -
23 g2685.t10 Coils Coil Coil 528 548 -
21 g2685.t10 Gene3D G3DSA:3.30.420.40 - 32 210 3.2E-154
20 g2685.t10 Gene3D G3DSA:3.30.420.40 - 211 363 3.2E-154
19 g2685.t10 Gene3D G3DSA:3.90.640.10 Actin; Chain A 255 338 3.2E-154
18 g2685.t10 Gene3D G3DSA:2.60.34.10 Substrate Binding Domain Of DNAk; Chain A 364 454 2.3E-41
22 g2685.t10 Gene3D G3DSA:1.20.1270.10 - 455 559 5.7E-35
33 g2685.t10 MobiDBLite mobidb-lite consensus disorder prediction 555 578 -
4 g2685.t10 PANTHER PTHR19375 HEAT SHOCK PROTEIN 70KDA 18 363 0.0
6 g2685.t10 PANTHER PTHR19375:SF380 ENDOPLASMIC RETICULUM CHAPERONE BIP 18 363 0.0
3 g2685.t10 PANTHER PTHR19375 HEAT SHOCK PROTEIN 70KDA 364 564 0.0
5 g2685.t10 PANTHER PTHR19375:SF380 ENDOPLASMIC RETICULUM CHAPERONE BIP 364 564 0.0
10 g2685.t10 PRINTS PR00301 70kDa heat shock protein signature 31 44 2.7E-38
9 g2685.t10 PRINTS PR00301 70kDa heat shock protein signature 59 71 2.7E-38
11 g2685.t10 PRINTS PR00301 70kDa heat shock protein signature 82 90 2.7E-38
12 g2685.t10 PRINTS PR00301 70kDa heat shock protein signature 169 189 2.7E-38
8 g2685.t10 PRINTS PR00301 70kDa heat shock protein signature 229 239 2.7E-38
7 g2685.t10 PRINTS PR00301 70kDa heat shock protein signature 357 373 2.7E-38
1 g2685.t10 Pfam PF00012 Hsp70 protein 32 363 1.7E-158
2 g2685.t10 Pfam PF00012 Hsp70 protein 364 558 3.2E-57
26 g2685.t10 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
27 g2685.t10 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
28 g2685.t10 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 16 -
29 g2685.t10 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 20 -
25 g2685.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 578 -
31 g2685.t10 ProSitePatterns PS00297 Heat shock hsp70 proteins family signature 1. 35 42 -
32 g2685.t10 ProSitePatterns PS00329 Heat shock hsp70 proteins family signature 2. 223 236 -
16 g2685.t10 SUPERFAMILY SSF53067 Actin-like ATPase domain 30 214 6.91E-72
15 g2685.t10 SUPERFAMILY SSF53067 Actin-like ATPase domain 218 363 4.16E-46
14 g2685.t10 SUPERFAMILY SSF100920 Heat shock protein 70kD (HSP70), peptide-binding domain 364 488 5.49E-47
13 g2685.t10 SUPERFAMILY SSF100934 Heat shock protein 70kD (HSP70), C-terminal subdomain 482 564 9.16E-26
17 g2685.t10 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

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