Gene loci information

Transcript annotation

  • This transcript has been annotated as DnaJ homolog subfamily A member 1.

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 g553 g553.t4 isoform g553.t4 4028247 4030708
chr_3 g553 g553.t4 exon g553.t4.exon1 4028247 4029728
chr_3 g553 g553.t4 TTS g553.t4 4028265 4028265
chr_3 g553 g553.t4 cds g553.t4.CDS1 4028825 4029728
chr_3 g553 g553.t4 exon g553.t4.exon2 4030225 4030708
chr_3 g553 g553.t4 cds g553.t4.CDS2 4030225 4030382
chr_3 g553 g553.t4 TSS g553.t4 4030963 4030963

Sequences

>g553.t4 Gene=g553 Length=1966
ATGGTGAAAGAAACAGGATATTATGATATTTTAGGTAAGTAAACCTGATAGCTTGCTTTT
ATAGCAAATACATTTTTGTGCTCTATAATTAATTGTCTCTAATCGATTTAATTTCATTTA
ATAGGCGTAAAGCCAAACTGCTCAAATGATGACCTCAAGAAGGCCTACAGAAAGCTTGCA
TTGAAATATCATCCAGACAAAGTAAGTTTTTCTCATTTCATAGTAATACGAACGTTAAAA
ATTACATCATAATGGTGAAATGGTTTTAAATAATTCATATTTCCTTCTAGAATCCTAATG
AAGGTGAAAAGTTCAAACAGATCTCAATGGCTTATGAAGTCCTCTCTGATCCAGAAAAAC
GACAAATTTATGACGAAGGTGGCGAGTCTGCGATCAAAAAAGGAGCTGGAGGTGGTGGCG
GCGGTTTCCACAGTCCTATGGATCTTTTCGATATGTTCTTTGGAGGCGGATTTGGTGGTG
GCAGACAACGCGAACGTAAAGGAAAAGATTTGGTTCACCAAATGCAAGTGTCGTTGGAAG
AAATATACAATGGAGCTGTACGCAAATTGGCTCTTCAAAAGAATGTCATTTGCGAGAAAT
GTGAAGGTCGTGGTGGAAAGAAAGGAGCTGTTGAAACTTGCGGCACTTGTCAAGGCAAAG
GTGTTGAAGTGAAAATTCAGCAAATCATGCCTGGATTTGTTCAAAAACATGAGCAAATTT
GCCGGGCATGTCAAGGACAAGGAGAAATCATCAATGCAAAAGACCGTTGCAAGACTTGTA
ATGGCAAAAAGACAGTGCGTGATAGGAAAATTCTCGAAGTTCATATTGAAAAGGGAATGC
AAGATGGTCAGAGAATAGTCTTCAACGGTGAAGGTGATCAAGAACCCGATTTACAACCAG
GCGATATCATTATCGTTTTGGATGTGAAAAAGCATCCAGTTTTCCAATTTAGCAATGGAA
CTGATCTTGCAATGGTTATGGATCTGCAATTGGTTGAAGCACTCTGCGGTTTTCAGAAAG
TCATCAAGACACTTGATCAACGTGATTTAGTGATTACTAGCCTTCCAGGTGAAGTAATTA
AAGACAATGAAATCAAGTGTGTGATGGGCGAGGGTATGCCAGAATACAAAAATCCATTCG
AGAAAGGTCGTTTGATTATTCAGTTTAATGTTGTATTTCCAAATGCAATTCCTCCTGAGT
ATATTCCTACTCTTGAACGATGCTTACCTTCACGACCACAAGTTGACATACCCATCACTG
CTGAAGAATGTATGCTTTCAAATTACGATCCCAATGCAGAGTCACAGCGACGACACAGAG
AAGCATATGAGGAAGATGATGAGCATTATCATCGTGGACCTCGTGTTCAACAATGTGCTA
CATCGTAAATATATAAGAGTCGTAGAATTATTTAACCATCGTTTCTCGCAACAAACCCGG
AAATGAAGTTCTTTAAATTTAAAATTGATTCGTATATATGAAGGAAAAATGCAATTTACC
ATCCAGCAAGAAAAAGCATAATAATAACTTATTTCATTCTATTCATATGTATTGCATTTT
CAAATCACTCATATTTTGTTTTCTCACTCTCACTATATTTTATATGCATAATAATAATGT
CCTTATTTTCTCTAAGTATGTGTTGAGATGAACGGAAAAATAAATAGATGAGGATTAAAC
TGTTAATGTAAAATTATAATACATAGAAATTACATGCTAGCAATGAAAATAATCACATAC
CGTAGAATTTTTATGTTGAACTCATTTTTTTTTGTAACGTTAACAGATATAAATTCACAT
GCGTCTATGTTGATTATTAGCTTAACAATTAAAATTTCCTTTGACGTCTATAAGTTAAAA
TAGATTATTTGAATTTCTTATTTTTAAGTTCATTCCTAAATTTAAACAGAAACAATACAC
AATATTCTAATAAAGATTATAGAAAATTAATTTAATGGTTTTTCTT

>g553.t4 Gene=g553 Length=353
MAYEVLSDPEKRQIYDEGGESAIKKGAGGGGGGFHSPMDLFDMFFGGGFGGGRQRERKGK
DLVHQMQVSLEEIYNGAVRKLALQKNVICEKCEGRGGKKGAVETCGTCQGKGVEVKIQQI
MPGFVQKHEQICRACQGQGEIINAKDRCKTCNGKKTVRDRKILEVHIEKGMQDGQRIVFN
GEGDQEPDLQPGDIIIVLDVKKHPVFQFSNGTDLAMVMDLQLVEALCGFQKVIKTLDQRD
LVITSLPGEVIKDNEIKCVMGEGMPEYKNPFEKGRLIIQFNVVFPNAIPPEYIPTLERCL
PSRPQVDIPITAEECMLSNYDPNAESQRRHREAYEEDDEHYHRGPRVQQCATS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g553.t4 CDD cd10747 DnaJ_C 60 285 1.17503E-41
15 g553.t4 CDD cd10719 DnaJ_zf 89 155 1.11733E-19
12 g553.t4 Gene3D G3DSA:1.10.287.110 - 1 55 2.7E-8
11 g553.t4 Gene3D G3DSA:2.10.230.10 - 91 155 1.5E-20
13 g553.t4 Gene3D G3DSA:2.60.260.20 Urease metallochaperone UreE 208 286 1.8E-21
10 g553.t4 MobiDBLite mobidb-lite consensus disorder prediction 321 353 -
9 g553.t4 MobiDBLite mobidb-lite consensus disorder prediction 324 345 -
3 g553.t4 PANTHER PTHR43888 DNAJ-LIKE-2, ISOFORM A-RELATED 2 348 8.6E-147
4 g553.t4 PANTHER PTHR43888:SF9 DNAJ HOMOLOG SUBFAMILY A MEMBER 4 2 348 8.6E-147
1 g553.t4 Pfam PF01556 DnaJ C terminal domain 63 285 2.6E-40
2 g553.t4 Pfam PF00684 DnaJ central domain 89 155 2.3E-15
14 g553.t4 ProSiteProfiles PS51188 Zinc finger CR-type profile. 76 160 23.622
8 g553.t4 SUPERFAMILY SSF46565 Chaperone J-domain 2 53 4.71E-9
7 g553.t4 SUPERFAMILY SSF49493 HSP40/DnaJ peptide-binding domain 61 204 7.85E-19
5 g553.t4 SUPERFAMILY SSF57938 DnaJ/Hsp40 cysteine-rich domain 86 158 1.23E-17
6 g553.t4 SUPERFAMILY SSF49493 HSP40/DnaJ peptide-binding domain 210 290 1.7E-15

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g553/g553.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g553.t4.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006457 protein folding BP
GO:0051082 unfolded protein binding MF
GO:0031072 heat shock protein binding 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