Gene loci information

Transcript annotation

  • This transcript has been annotated as Heat shock protein 60A.

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 g2580 g2580.t6 isoform g2580.t6 18832218 18833370
chr_3 g2580 g2580.t6 exon g2580.t6.exon1 18832218 18833370
chr_3 g2580 g2580.t6 cds g2580.t6.CDS1 18832218 18833369
chr_3 g2580 g2580.t6 TSS g2580.t6 18833742 18833742
chr_3 g2580 g2580.t6 TTS g2580.t6 NA NA

Sequences

>g2580.t6 Gene=g2580 Length=1153
GATGTATCGACTTCCGACAGTTTTAAGAGCTGCCACAGCTCGTCAGCTTGCATTTCGTAC
ATATGCTAAAGATGTGAAATTTGGTGGAGATGTTCGTGCTATTATGTTGCAAGGAGTTGA
CATTTTAGCAGATGCAGTCGCTGTTACTATGGGTCCAAAAGGCCGAAATGTTATCTTAGA
GCAATCATGGGGTTCACCTAAAATCACAAAAGACGGAGTAACAGTTGCTAAAGGAATTGA
ATTAAAAGACAAATTCCAAAATATCGGAGCTAAACTTGTACAAGATGTTGCTAACAATAC
AAATGAAGAAGCTGGTGATGGCACCACAACAGCAACTGTTCTCGCTCGAGCAATTGCAAA
AGAAGGCTTCGAAAAAATTTCAAAAGGTGCAAATCCAGTTGAAATTCGTCGTGGAGTTAT
GATGGCAGTAGATGCTGTGAAAGAAAAACTAAAAACTCTTTCACGACCGGTCACAACACC
AGAAGAAATTGCACAAGTAGCAACTATCTCAGCAAATGGTGATCGAGCAATTGGAGATCT
CATTAGTGATGCAATGAAACGTGTAGGAAAAGATGGAGTTATCACAGTGAAAGATGGCAA
AACATTAAACGATGAACTTGAAGTAATTGAGGGCATGAAATTTGATCGTGGTTATATTTC
ACCATATTTCATTAACTCATCAAAAGGAGCCAAAGTAGAATTTCAAGATGCTCTCTTGCT
TTTATCGGAAAAGAAAATCTCAACAGTTCAAAGTATCATTCCTGCACTTGAACTTGCCAA
TCAACAGAGAAAACCACTTGTCATCATTGCTGAAGATCTTGATGGTGAAGCACTTTCAAC
TTTGGTTGTTAACAGATTAAAGATTGGACTTCAAGTTGCTGCTGTTAAAGCACCAGGTTT
TGGTGACAACAGAAAATCAACTTTGGCAGACATGGCGATTGCTACTGGCGGAATTGTTTT
CGGAGATGAAGCCAATTTAGTTAAAATTGAAGATGTCCAATTATCAGATTTTGGTCAAGT
TGGTGAAGTTGTCATTACAAAAGACGATACATTGTTGCTCAAAGGAAAAGGAGACAAGGC
TCATGTTGATCAACGCGCACAACAAATTAGAGATCAAATTGCTGAAACCACATCAGAATA
TGAAAAGGAAAAA

>g2580.t6 Gene=g2580 Length=384
MYRLPTVLRAATARQLAFRTYAKDVKFGGDVRAIMLQGVDILADAVAVTMGPKGRNVILE
QSWGSPKITKDGVTVAKGIELKDKFQNIGAKLVQDVANNTNEEAGDGTTTATVLARAIAK
EGFEKISKGANPVEIRRGVMMAVDAVKEKLKTLSRPVTTPEEIAQVATISANGDRAIGDL
ISDAMKRVGKDGVITVKDGKTLNDELEVIEGMKFDRGYISPYFINSSKGAKVEFQDALLL
LSEKKISTVQSIIPALELANQQRKPLVIIAEDLDGEALSTLVVNRLKIGLQVAAVKAPGF
GDNRKSTLADMAIATGGIVFGDEANLVKIEDVQLSDFGQVGEVVITKDDTLLLKGKGDKA
HVDQRAQQIRDQIAETTSEYEKEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2580.t6 CDD cd03344 GroEL 23 384 0.0
12 g2580.t6 Coils Coil Coil 366 384 -
10 g2580.t6 Gene3D G3DSA:1.10.560.10 GROEL 21 194 7.0E-50
11 g2580.t6 Gene3D G3DSA:3.50.7.10 GroEL 195 384 2.7E-78
2 g2580.t6 PANTHER PTHR45633 60 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL 18 384 1.7E-185
3 g2580.t6 PANTHER PTHR45633:SF3 60 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL 18 384 1.7E-185
6 g2580.t6 PRINTS PR00298 60kDa chaperonin signature 46 72 5.4E-45
5 g2580.t6 PRINTS PR00298 60kDa chaperonin signature 102 129 5.4E-45
4 g2580.t6 PRINTS PR00298 60kDa chaperonin signature 287 310 5.4E-45
7 g2580.t6 PRINTS PR00298 60kDa chaperonin signature 370 384 5.4E-45
1 g2580.t6 Pfam PF00118 TCP-1/cpn60 chaperonin family 42 356 8.4E-48
9 g2580.t6 SUPERFAMILY SSF48592 GroEL equatorial domain-like 22 247 1.96E-58
8 g2580.t6 SUPERFAMILY SSF52029 GroEL apical domain-like 203 384 3.44E-66

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:0042026 protein refolding BP
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