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.t1 TTS g553.t1 4028265 4028265
chr_3 g553 g553.t1 isoform g553.t1 4028825 4030708
chr_3 g553 g553.t1 exon g553.t1.exon1 4028825 4029728
chr_3 g553 g553.t1 cds g553.t1.CDS1 4028825 4029728
chr_3 g553 g553.t1 exon g553.t1.exon2 4030225 4030418
chr_3 g553 g553.t1 cds g553.t1.CDS2 4030225 4030418
chr_3 g553 g553.t1 exon g553.t1.exon3 4030508 4030584
chr_3 g553 g553.t1 cds g553.t1.CDS3 4030508 4030584
chr_3 g553 g553.t1 exon g553.t1.exon4 4030675 4030708
chr_3 g553 g553.t1 cds g553.t1.CDS4 4030675 4030708
chr_3 g553 g553.t1 TSS g553.t1 4030963 4030963

Sequences

>g553.t1 Gene=g553 Length=1209
ATGGTGAAAGAAACAGGATATTATGATATTTTAGGCGTAAAGCCAAACTGCTCAAATGAT
GACCTCAAGAAGGCCTACAGAAAGCTTGCATTGAAATATCATCCAGACAAAAATCCTAAT
GAAGGTGAAAAGTTCAAACAGATCTCAATGGCTTATGAAGTCCTCTCTGATCCAGAAAAA
CGACAAATTTATGACGAAGGTGGCGAGTCTGCGATCAAAAAAGGAGCTGGAGGTGGTGGC
GGCGGTTTCCACAGTCCTATGGATCTTTTCGATATGTTCTTTGGAGGCGGATTTGGTGGT
GGCAGACAACGCGAACGTAAAGGAAAAGATTTGGTTCACCAAATGCAAGTGTCGTTGGAA
GAAATATACAATGGAGCTGTACGCAAATTGGCTCTTCAAAAGAATGTCATTTGCGAGAAA
TGTGAAGGTCGTGGTGGAAAGAAAGGAGCTGTTGAAACTTGCGGCACTTGTCAAGGCAAA
GGTGTTGAAGTGAAAATTCAGCAAATCATGCCTGGATTTGTTCAAAAACATGAGCAAATT
TGCCGGGCATGTCAAGGACAAGGAGAAATCATCAATGCAAAAGACCGTTGCAAGACTTGT
AATGGCAAAAAGACAGTGCGTGATAGGAAAATTCTCGAAGTTCATATTGAAAAGGGAATG
CAAGATGGTCAGAGAATAGTCTTCAACGGTGAAGGTGATCAAGAACCCGATTTACAACCA
GGCGATATCATTATCGTTTTGGATGTGAAAAAGCATCCAGTTTTCCAATTTAGCAATGGA
ACTGATCTTGCAATGGTTATGGATCTGCAATTGGTTGAAGCACTCTGCGGTTTTCAGAAA
GTCATCAAGACACTTGATCAACGTGATTTAGTGATTACTAGCCTTCCAGGTGAAGTAATT
AAAGACAATGAAATCAAGTGTGTGATGGGCGAGGGTATGCCAGAATACAAAAATCCATTC
GAGAAAGGTCGTTTGATTATTCAGTTTAATGTTGTATTTCCAAATGCAATTCCTCCTGAG
TATATTCCTACTCTTGAACGATGCTTACCTTCACGACCACAAGTTGACATACCCATCACT
GCTGAAGAATGTATGCTTTCAAATTACGATCCCAATGCAGAGTCACAGCGACGACACAGA
GAAGCATATGAGGAAGATGATGAGCATTATCATCGTGGACCTCGTGTTCAACAATGTGCT
ACATCGTAA

>g553.t1 Gene=g553 Length=402
MVKETGYYDILGVKPNCSNDDLKKAYRKLALKYHPDKNPNEGEKFKQISMAYEVLSDPEK
RQIYDEGGESAIKKGAGGGGGGFHSPMDLFDMFFGGGFGGGRQRERKGKDLVHQMQVSLE
EIYNGAVRKLALQKNVICEKCEGRGGKKGAVETCGTCQGKGVEVKIQQIMPGFVQKHEQI
CRACQGQGEIINAKDRCKTCNGKKTVRDRKILEVHIEKGMQDGQRIVFNGEGDQEPDLQP
GDIIIVLDVKKHPVFQFSNGTDLAMVMDLQLVEALCGFQKVIKTLDQRDLVITSLPGEVI
KDNEIKCVMGEGMPEYKNPFEKGRLIIQFNVVFPNAIPPEYIPTLERCLPSRPQVDIPIT
AEECMLSNYDPNAESQRRHREAYEEDDEHYHRGPRVQQCATS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g553.t1 CDD cd06257 DnaJ 7 57 2.27234E-24
19 g553.t1 CDD cd10747 DnaJ_C 109 334 1.95035E-41
18 g553.t1 CDD cd10719 DnaJ_zf 138 204 4.93255E-20
15 g553.t1 Gene3D G3DSA:1.10.287.110 - 3 104 6.0E-33
14 g553.t1 Gene3D G3DSA:2.10.230.10 - 140 204 1.9E-20
16 g553.t1 Gene3D G3DSA:2.60.260.20 Urease metallochaperone UreE 257 335 2.2E-21
6 g553.t1 Hamap MF_01152 Chaperone protein DnaJ [dnaJ]. 3 382 26.86924
23 g553.t1 MobiDBLite mobidb-lite consensus disorder prediction 370 402 -
22 g553.t1 MobiDBLite mobidb-lite consensus disorder prediction 373 394 -
4 g553.t1 PANTHER PTHR43888 DNAJ-LIKE-2, ISOFORM A-RELATED 1 397 6.3E-179
5 g553.t1 PANTHER PTHR43888:SF9 DNAJ HOMOLOG SUBFAMILY A MEMBER 4 1 397 6.3E-179
9 g553.t1 PRINTS PR00625 DnaJ domain signature 8 26 1.4E-18
7 g553.t1 PRINTS PR00625 DnaJ domain signature 26 41 1.4E-18
8 g553.t1 PRINTS PR00625 DnaJ domain signature 60 79 1.4E-18
3 g553.t1 Pfam PF00226 DnaJ domain 7 65 1.0E-26
1 g553.t1 Pfam PF01556 DnaJ C terminal domain 112 334 3.8E-40
2 g553.t1 Pfam PF00684 DnaJ central domain 138 204 2.8E-15
21 g553.t1 ProSitePatterns PS00636 Nt-dnaJ domain signature. 45 64 -
25 g553.t1 ProSiteProfiles PS50076 dnaJ domain profile. 6 68 22.989
24 g553.t1 ProSiteProfiles PS51188 Zinc finger CR-type profile. 125 209 23.622
20 g553.t1 SMART SM00271 dnaj_3 5 60 2.7E-29
13 g553.t1 SUPERFAMILY SSF46565 Chaperone J-domain 2 102 2.88E-36
11 g553.t1 SUPERFAMILY SSF49493 HSP40/DnaJ peptide-binding domain 104 256 7.46E-19
10 g553.t1 SUPERFAMILY SSF57938 DnaJ/Hsp40 cysteine-rich domain 135 207 1.57E-17
12 g553.t1 SUPERFAMILY SSF49493 HSP40/DnaJ peptide-binding domain 259 339 2.22E-15

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g553/g553.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g553.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006457 protein folding BP
GO:0005524 ATP binding MF
GO:0051082 unfolded protein binding MF
GO:0031072 heat shock protein binding MF
GO:0009408 response to heat BP

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