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.t1 TTS g2580.t1 18831183 18831183
chr_3 g2580 g2580.t1 isoform g2580.t1 18831603 18833369
chr_3 g2580 g2580.t1 exon g2580.t1.exon1 18831603 18831758
chr_3 g2580 g2580.t1 cds g2580.t1.CDS1 18831603 18831758
chr_3 g2580 g2580.t1 exon g2580.t1.exon2 18831816 18833369
chr_3 g2580 g2580.t1 cds g2580.t1.CDS2 18831816 18833369
chr_3 g2580 g2580.t1 TSS g2580.t1 18833742 18833742

Sequences

>g2580.t1 Gene=g2580 Length=1710
ATGTATCGACTTCCGACAGTTTTAAGAGCTGCCACAGCTCGTCAGCTTGCATTTCGTACA
TATGCTAAAGATGTGAAATTTGGTGGAGATGTTCGTGCTATTATGTTGCAAGGAGTTGAC
ATTTTAGCAGATGCAGTCGCTGTTACTATGGGTCCAAAAGGCCGAAATGTTATCTTAGAG
CAATCATGGGGTTCACCTAAAATCACAAAAGACGGAGTAACAGTTGCTAAAGGAATTGAA
TTAAAAGACAAATTCCAAAATATCGGAGCTAAACTTGTACAAGATGTTGCTAACAATACA
AATGAAGAAGCTGGTGATGGCACCACAACAGCAACTGTTCTCGCTCGAGCAATTGCAAAA
GAAGGCTTCGAAAAAATTTCAAAAGGTGCAAATCCAGTTGAAATTCGTCGTGGAGTTATG
ATGGCAGTAGATGCTGTGAAAGAAAAACTAAAAACTCTTTCACGACCGGTCACAACACCA
GAAGAAATTGCACAAGTAGCAACTATCTCAGCAAATGGTGATCGAGCAATTGGAGATCTC
ATTAGTGATGCAATGAAACGTGTAGGAAAAGATGGAGTTATCACAGTGAAAGATGGCAAA
ACATTAAACGATGAACTTGAAGTAATTGAGGGCATGAAATTTGATCGTGGTTATATTTCA
CCATATTTCATTAACTCATCAAAAGGAGCCAAAGTAGAATTTCAAGATGCTCTCTTGCTT
TTATCGGAAAAGAAAATCTCAACAGTTCAAAGTATCATTCCTGCACTTGAACTTGCCAAT
CAACAGAGAAAACCACTTGTCATCATTGCTGAAGATCTTGATGGTGAAGCACTTTCAACT
TTGGTTGTTAACAGATTAAAGATTGGACTTCAAGTTGCTGCTGTTAAAGCACCAGGTTTT
GGTGACAACAGAAAATCAACTTTGGCAGACATGGCGATTGCTACTGGCGGAATTGTTTTC
GGAGATGAAGCCAATTTAGTTAAAATTGAAGATGTCCAATTATCAGATTTTGGTCAAGTT
GGTGAAGTTGTCATTACAAAAGACGATACATTGTTGCTCAAAGGAAAAGGAGACAAGGCT
CATGTTGATCAACGCGCACAACAAATTAGAGATCAAATTGCTGAAACCACATCAGAATAT
GAAAAGGAAAAACTTCAAGAAAGATTAGCCAGATTGTCATCAGGTGTTGCTGTATTGAAA
GTTGGTGGATCAAGTGAAGTTGAAGTCAATGAAAAGAAAGACCGTGTTAATGATGCCCTC
TGCGCTACTCGTGCTGCAGTTGAAGAAGGAATCGTCCCCGGTGGTGGAACTGCACTCTTG
AGATGTATTCCAGCATTGAATGATCTTAAAGGATCAAATGCTGATCAAACTGTCGGTATT
GAAATTGTCAAAAAATCACTCCGCATGCCTTGCCTTCAAATTGCCAAAAATACAGGAGTC
GATGGGTCAGTTGTTGTCGCTAAGGTCGAAGAACAGACAGGAGATTTCGGATATGATGCA
TTAAATAACGAGTATGTGAATATGTTTGAAAAGGGTATCATTGATCCAACAAAGGTTGTC
CGCACAGCTTTAACTGATGCAGCTGGTGTTGCTTCATTACTCACAACTGCCGAATGTGTT
GTATGTGAGATTCCAAAAGAAGAACCTGCAAATCCAATGGCCGGTATGGGTGGCATGGGT
GGAATGGGAGGTATGGGAGGAATGATGTAA

>g2580.t1 Gene=g2580 Length=569
MYRLPTVLRAATARQLAFRTYAKDVKFGGDVRAIMLQGVDILADAVAVTMGPKGRNVILE
QSWGSPKITKDGVTVAKGIELKDKFQNIGAKLVQDVANNTNEEAGDGTTTATVLARAIAK
EGFEKISKGANPVEIRRGVMMAVDAVKEKLKTLSRPVTTPEEIAQVATISANGDRAIGDL
ISDAMKRVGKDGVITVKDGKTLNDELEVIEGMKFDRGYISPYFINSSKGAKVEFQDALLL
LSEKKISTVQSIIPALELANQQRKPLVIIAEDLDGEALSTLVVNRLKIGLQVAAVKAPGF
GDNRKSTLADMAIATGGIVFGDEANLVKIEDVQLSDFGQVGEVVITKDDTLLLKGKGDKA
HVDQRAQQIRDQIAETTSEYEKEKLQERLARLSSGVAVLKVGGSSEVEVNEKKDRVNDAL
CATRAAVEEGIVPGGGTALLRCIPALNDLKGSNADQTVGIEIVKKSLRMPCLQIAKNTGV
DGSVVVAKVEEQTGDFGYDALNNEYVNMFEKGIIDPTKVVRTALTDAAGVASLLTTAECV
VCEIPKEEPANPMAGMGGMGGMGGMGGMM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g2580.t1 CDD cd03344 GroEL 23 543 0.0
16 g2580.t1 Coils Coil Coil 366 386 -
13 g2580.t1 Gene3D G3DSA:1.10.560.10 GROEL 26 541 1.1E-230
15 g2580.t1 Gene3D G3DSA:3.30.260.10 GROEL 156 430 1.1E-230
14 g2580.t1 Gene3D G3DSA:3.50.7.10 GroEL 211 393 1.1E-230
4 g2580.t1 Hamap MF_00600 60 kDa chaperonin [groL]. 21 565 36.351784
2 g2580.t1 PANTHER PTHR45633 60 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL 18 548 2.0E-269
3 g2580.t1 PANTHER PTHR45633:SF3 60 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL 18 548 2.0E-269
7 g2580.t1 PRINTS PR00298 60kDa chaperonin signature 46 72 6.3E-67
6 g2580.t1 PRINTS PR00298 60kDa chaperonin signature 102 129 6.3E-67
5 g2580.t1 PRINTS PR00298 60kDa chaperonin signature 287 310 6.3E-67
8 g2580.t1 PRINTS PR00298 60kDa chaperonin signature 370 395 6.3E-67
9 g2580.t1 PRINTS PR00298 60kDa chaperonin signature 418 439 6.3E-67
1 g2580.t1 Pfam PF00118 TCP-1/cpn60 chaperonin family 42 542 1.6E-82
18 g2580.t1 ProSitePatterns PS00296 Chaperonins cpn60 signature. 425 436 -
12 g2580.t1 SUPERFAMILY SSF48592 GroEL equatorial domain-like 26 541 1.5E-74
11 g2580.t1 SUPERFAMILY SSF54849 GroEL-intermediate domain like 156 222 3.2E-26
10 g2580.t1 SUPERFAMILY SSF52029 GroEL apical domain-like 203 396 2.49E-72
19 g2580.t1 TIGRFAM TIGR02348 GroEL: chaperonin GroL 22 547 4.9E-216

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:0006457 protein folding BP
GO:0005524 ATP binding MF
GO:0042026 protein refolding BP
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