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.t14 TTS g553.t14 4028265 4028265
chr_3 g553 g553.t14 isoform g553.t14 4028467 4030935
chr_3 g553 g553.t14 exon g553.t14.exon1 4028467 4029728
chr_3 g553 g553.t14 cds g553.t14.CDS1 4028825 4029728
chr_3 g553 g553.t14 exon g553.t14.exon2 4030225 4030397
chr_3 g553 g553.t14 cds g553.t14.CDS2 4030225 4030382
chr_3 g553 g553.t14 exon g553.t14.exon3 4030675 4030727
chr_3 g553 g553.t14 exon g553.t14.exon4 4030887 4030935
chr_3 g553 g553.t14 TSS g553.t14 4030963 4030963

Sequences

>g553.t14 Gene=g553 Length=1537
TTTTAAGTAAAACTTGAACAGTTTCAGACGTTTTTGCGAGAGAAAAAGGTTAATATAATT
CTACAAACATGGTGAAAGAAACAGGATATTATGATATTTTAGTTCAAACAGATCTCAATG
GCTTATGAAGTCCTCTCTGATCCAGAAAAACGACAAATTTATGACGAAGGTGGCGAGTCT
GCGATCAAAAAAGGAGCTGGAGGTGGTGGCGGCGGTTTCCACAGTCCTATGGATCTTTTC
GATATGTTCTTTGGAGGCGGATTTGGTGGTGGCAGACAACGCGAACGTAAAGGAAAAGAT
TTGGTTCACCAAATGCAAGTGTCGTTGGAAGAAATATACAATGGAGCTGTACGCAAATTG
GCTCTTCAAAAGAATGTCATTTGCGAGAAATGTGAAGGTCGTGGTGGAAAGAAAGGAGCT
GTTGAAACTTGCGGCACTTGTCAAGGCAAAGGTGTTGAAGTGAAAATTCAGCAAATCATG
CCTGGATTTGTTCAAAAACATGAGCAAATTTGCCGGGCATGTCAAGGACAAGGAGAAATC
ATCAATGCAAAAGACCGTTGCAAGACTTGTAATGGCAAAAAGACAGTGCGTGATAGGAAA
ATTCTCGAAGTTCATATTGAAAAGGGAATGCAAGATGGTCAGAGAATAGTCTTCAACGGT
GAAGGTGATCAAGAACCCGATTTACAACCAGGCGATATCATTATCGTTTTGGATGTGAAA
AAGCATCCAGTTTTCCAATTTAGCAATGGAACTGATCTTGCAATGGTTATGGATCTGCAA
TTGGTTGAAGCACTCTGCGGTTTTCAGAAAGTCATCAAGACACTTGATCAACGTGATTTA
GTGATTACTAGCCTTCCAGGTGAAGTAATTAAAGACAATGAAATCAAGTGTGTGATGGGC
GAGGGTATGCCAGAATACAAAAATCCATTCGAGAAAGGTCGTTTGATTATTCAGTTTAAT
GTTGTATTTCCAAATGCAATTCCTCCTGAGTATATTCCTACTCTTGAACGATGCTTACCT
TCACGACCACAAGTTGACATACCCATCACTGCTGAAGAATGTATGCTTTCAAATTACGAT
CCCAATGCAGAGTCACAGCGACGACACAGAGAAGCATATGAGGAAGATGATGAGCATTAT
CATCGTGGACCTCGTGTTCAACAATGTGCTACATCGTAAATATATAAGAGTCGTAGAATT
ATTTAACCATCGTTTCTCGCAACAAACCCGGAAATGAAGTTCTTTAAATTTAAAATTGAT
TCGTATATATGAAGGAAAAATGCAATTTACCATCCAGCAAGAAAAAGCATAATAATAACT
TATTTCATTCTATTCATATGTATTGCATTTTCAAATCACTCATATTTTGTTTTCTCACTC
TCACTATATTTTATATGCATAATAATAATGTCCTTATTTTCTCTAAGTATGTGTTGAGAT
GAACGGAAAAATAAATAGATGAGGATTAAACTGTTAATGTAAAATTATAATACATAGAAA
TTACATGCTAGCAATGAAAATAATCACATACCGTAGA

>g553.t14 Gene=g553 Length=353
MAYEVLSDPEKRQIYDEGGESAIKKGAGGGGGGFHSPMDLFDMFFGGGFGGGRQRERKGK
DLVHQMQVSLEEIYNGAVRKLALQKNVICEKCEGRGGKKGAVETCGTCQGKGVEVKIQQI
MPGFVQKHEQICRACQGQGEIINAKDRCKTCNGKKTVRDRKILEVHIEKGMQDGQRIVFN
GEGDQEPDLQPGDIIIVLDVKKHPVFQFSNGTDLAMVMDLQLVEALCGFQKVIKTLDQRD
LVITSLPGEVIKDNEIKCVMGEGMPEYKNPFEKGRLIIQFNVVFPNAIPPEYIPTLERCL
PSRPQVDIPITAEECMLSNYDPNAESQRRHREAYEEDDEHYHRGPRVQQCATS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g553.t14 CDD cd10747 DnaJ_C 60 285 1.17503E-41
15 g553.t14 CDD cd10719 DnaJ_zf 89 155 1.11733E-19
12 g553.t14 Gene3D G3DSA:1.10.287.110 - 1 55 2.7E-8
11 g553.t14 Gene3D G3DSA:2.10.230.10 - 91 155 1.5E-20
13 g553.t14 Gene3D G3DSA:2.60.260.20 Urease metallochaperone UreE 208 286 1.8E-21
10 g553.t14 MobiDBLite mobidb-lite consensus disorder prediction 321 353 -
9 g553.t14 MobiDBLite mobidb-lite consensus disorder prediction 324 345 -
3 g553.t14 PANTHER PTHR43888 DNAJ-LIKE-2, ISOFORM A-RELATED 2 348 8.6E-147
4 g553.t14 PANTHER PTHR43888:SF9 DNAJ HOMOLOG SUBFAMILY A MEMBER 4 2 348 8.6E-147
1 g553.t14 Pfam PF01556 DnaJ C terminal domain 63 285 2.6E-40
2 g553.t14 Pfam PF00684 DnaJ central domain 89 155 2.3E-15
14 g553.t14 ProSiteProfiles PS51188 Zinc finger CR-type profile. 76 160 23.622
8 g553.t14 SUPERFAMILY SSF46565 Chaperone J-domain 2 53 4.71E-9
7 g553.t14 SUPERFAMILY SSF49493 HSP40/DnaJ peptide-binding domain 61 204 7.85E-19
5 g553.t14 SUPERFAMILY SSF57938 DnaJ/Hsp40 cysteine-rich domain 86 158 1.23E-17
6 g553.t14 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.t14; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g553.t14.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