Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative DnaJ homolog subfamily A member 4.

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.t15 TTS g553.t15 4028265 4028265
chr_3 g553 g553.t15 isoform g553.t15 4028825 4030935
chr_3 g553 g553.t15 exon g553.t15.exon1 4028825 4029369
chr_3 g553 g553.t15 cds g553.t15.CDS1 4028825 4029369
chr_3 g553 g553.t15 exon g553.t15.exon2 4030235 4030418
chr_3 g553 g553.t15 cds g553.t15.CDS2 4030235 4030418
chr_3 g553 g553.t15 exon g553.t15.exon3 4030508 4030584
chr_3 g553 g553.t15 cds g553.t15.CDS3 4030508 4030584
chr_3 g553 g553.t15 exon g553.t15.exon4 4030675 4030727
chr_3 g553 g553.t15 cds g553.t15.CDS4 4030675 4030708
chr_3 g553 g553.t15 exon g553.t15.exon5 4030887 4030935
chr_3 g553 g553.t15 TSS g553.t15 4030963 4030963

Sequences

>g553.t15 Gene=g553 Length=908
TTTTAAGTAAAACTTGAACAGTTTCAGACGTTTTTGCGAGAGAAAAAGGTTAATATAATT
CTACAAACATGGTGAAAGAAACAGGATATTATGATATTTTAGGCGTAAAGCCAAACTGCT
CAAATGATGACCTCAAGAAGGCCTACAGAAAGCTTGCATTGAAATATCATCCAGACAAAA
ATCCTAATGAAGGTGAAAAGTTCAAACAGATCTCAATGGCTTATGAAGTCCTCTCTGATC
CAGAAAAACGACAAATTTATGACGAAGGTGGCGAGTCTGCGATCAAAAAAGGAGCTGGAG
GTGGTGGCGGCGGTTTCCACAGTCCTATGGATCTTTTCGATATGTTCTTTGGAGGCGGAT
TTGATGGTCAGAGAATAGTCTTCAACGGTGAAGGTGATCAAGAACCCGATTTACAACCAG
GCGATATCATTATCGTTTTGGATGTGAAAAAGCATCCAGTTTTCCAATTTAGCAATGGAA
CTGATCTTGCAATGGTTATGGATCTGCAATTGGTTGAAGCACTCTGCGGTTTTCAGAAAG
TCATCAAGACACTTGATCAACGTGATTTAGTGATTACTAGCCTTCCAGGTGAAGTAATTA
AAGACAATGAAATCAAGTGTGTGATGGGCGAGGGTATGCCAGAATACAAAAATCCATTCG
AGAAAGGTCGTTTGATTATTCAGTTTAATGTTGTATTTCCAAATGCAATTCCTCCTGAGT
ATATTCCTACTCTTGAACGATGCTTACCTTCACGACCACAAGTTGACATACCCATCACTG
CTGAAGAATGTATGCTTTCAAATTACGATCCCAATGCAGAGTCACAGCGACGACACAGAG
AAGCATATGAGGAAGATGATGAGCATTATCATCGTGGACCTCGTGTTCAACAATGTGCTA
CATCGTAA

>g553.t15 Gene=g553 Length=279
MVKETGYYDILGVKPNCSNDDLKKAYRKLALKYHPDKNPNEGEKFKQISMAYEVLSDPEK
RQIYDEGGESAIKKGAGGGGGGFHSPMDLFDMFFGGGFDGQRIVFNGEGDQEPDLQPGDI
IIVLDVKKHPVFQFSNGTDLAMVMDLQLVEALCGFQKVIKTLDQRDLVITSLPGEVIKDN
EIKCVMGEGMPEYKNPFEKGRLIIQFNVVFPNAIPPEYIPTLERCLPSRPQVDIPITAEE
CMLSNYDPNAESQRRHREAYEEDDEHYHRGPRVQQCATS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g553.t15 CDD cd06257 DnaJ 7 57 7.78911E-25
17 g553.t15 CDD cd10747 DnaJ_C 99 211 7.4119E-32
13 g553.t15 Gene3D G3DSA:1.10.287.110 - 3 100 1.4E-32
14 g553.t15 Gene3D G3DSA:2.60.260.20 Urease metallochaperone UreE 101 127 8.0E-7
15 g553.t15 Gene3D G3DSA:2.60.260.20 Urease metallochaperone UreE 134 212 1.2E-21
21 g553.t15 MobiDBLite mobidb-lite consensus disorder prediction 247 279 -
20 g553.t15 MobiDBLite mobidb-lite consensus disorder prediction 250 271 -
4 g553.t15 PANTHER PTHR43888 DNAJ-LIKE-2, ISOFORM A-RELATED 1 97 2.5E-113
6 g553.t15 PANTHER PTHR43888:SF9 DNAJ HOMOLOG SUBFAMILY A MEMBER 4 1 97 2.5E-113
3 g553.t15 PANTHER PTHR43888 DNAJ-LIKE-2, ISOFORM A-RELATED 99 274 2.5E-113
5 g553.t15 PANTHER PTHR43888:SF9 DNAJ HOMOLOG SUBFAMILY A MEMBER 4 99 274 2.5E-113
9 g553.t15 PRINTS PR00625 DnaJ domain signature 8 26 5.6E-19
7 g553.t15 PRINTS PR00625 DnaJ domain signature 26 41 5.6E-19
8 g553.t15 PRINTS PR00625 DnaJ domain signature 60 79 5.6E-19
2 g553.t15 Pfam PF00226 DnaJ domain 7 65 5.7E-27
1 g553.t15 Pfam PF01556 DnaJ C terminal domain 99 211 1.1E-26
19 g553.t15 ProSitePatterns PS00636 Nt-dnaJ domain signature. 45 64 -
22 g553.t15 ProSiteProfiles PS50076 dnaJ domain profile. 6 68 22.989
18 g553.t15 SMART SM00271 dnaj_3 5 60 2.7E-29
12 g553.t15 SUPERFAMILY SSF46565 Chaperone J-domain 2 105 1.26E-36
11 g553.t15 SUPERFAMILY SSF49493 HSP40/DnaJ peptide-binding domain 98 133 1.83E-6
10 g553.t15 SUPERFAMILY SSF49493 HSP40/DnaJ peptide-binding domain 136 216 1.11E-15

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g553/g553.t15; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g553.t15.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006457 protein folding BP
GO:0051082 unfolded 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