General information for g553.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DnaJ homolog subfamily A member 1.
Parent gene
- The parent gene g553 is located on chr_3: 4028825..4030935 (- strand)
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.t12 | isoform | g553.t12 | 4028247 | 4030935 |
| chr_3 | g553 | g553.t12 | exon | g553.t12.exon1 | 4028247 | 4029728 |
| chr_3 | g553 | g553.t12 | TTS | g553.t12 | 4028265 | 4028265 |
| chr_3 | g553 | g553.t12 | cds | g553.t12.CDS1 | 4028825 | 4029728 |
| chr_3 | g553 | g553.t12 | exon | g553.t12.exon2 | 4030225 | 4030418 |
| chr_3 | g553 | g553.t12 | cds | g553.t12.CDS2 | 4030225 | 4030382 |
| chr_3 | g553 | g553.t12 | exon | g553.t12.exon3 | 4030508 | 4030584 |
| chr_3 | g553 | g553.t12 | exon | g553.t12.exon4 | 4030671 | 4030727 |
| chr_3 | g553 | g553.t12 | exon | g553.t12.exon5 | 4030887 | 4030935 |
| chr_3 | g553 | g553.t12 | TSS | g553.t12 | 4030963 | 4030963 |
Sequences
>g553.t12 Gene=g553 Length=1859
TTTTAAGTAAAACTTGAACAGTTTCAGACGTTTTTGCGAGAGAAAAAGGTTAATATAATT
CTACAAACATGGTGAAAGAAACAGGATATTATGATATTTTAGGTAAGCGTAAAGCCAAAC
TGCTCAAATGATGACCTCAAGAAGGCCTACAGAAAGCTTGCATTGAAATATCATCCAGAC
AAAAATCCTAATGAAGGTGAAAAGTTCAAACAGATCTCAATGGCTTATGAAGTCCTCTCT
GATCCAGAAAAACGACAAATTTATGACGAAGGTGGCGAGTCTGCGATCAAAAAAGGAGCT
GGAGGTGGTGGCGGCGGTTTCCACAGTCCTATGGATCTTTTCGATATGTTCTTTGGAGGC
GGATTTGGTGGTGGCAGACAACGCGAACGTAAAGGAAAAGATTTGGTTCACCAAATGCAA
GTGTCGTTGGAAGAAATATACAATGGAGCTGTACGCAAATTGGCTCTTCAAAAGAATGTC
ATTTGCGAGAAATGTGAAGGTCGTGGTGGAAAGAAAGGAGCTGTTGAAACTTGCGGCACT
TGTCAAGGCAAAGGTGTTGAAGTGAAAATTCAGCAAATCATGCCTGGATTTGTTCAAAAA
CATGAGCAAATTTGCCGGGCATGTCAAGGACAAGGAGAAATCATCAATGCAAAAGACCGT
TGCAAGACTTGTAATGGCAAAAAGACAGTGCGTGATAGGAAAATTCTCGAAGTTCATATT
GAAAAGGGAATGCAAGATGGTCAGAGAATAGTCTTCAACGGTGAAGGTGATCAAGAACCC
GATTTACAACCAGGCGATATCATTATCGTTTTGGATGTGAAAAAGCATCCAGTTTTCCAA
TTTAGCAATGGAACTGATCTTGCAATGGTTATGGATCTGCAATTGGTTGAAGCACTCTGC
GGTTTTCAGAAAGTCATCAAGACACTTGATCAACGTGATTTAGTGATTACTAGCCTTCCA
GGTGAAGTAATTAAAGACAATGAAATCAAGTGTGTGATGGGCGAGGGTATGCCAGAATAC
AAAAATCCATTCGAGAAAGGTCGTTTGATTATTCAGTTTAATGTTGTATTTCCAAATGCA
ATTCCTCCTGAGTATATTCCTACTCTTGAACGATGCTTACCTTCACGACCACAAGTTGAC
ATACCCATCACTGCTGAAGAATGTATGCTTTCAAATTACGATCCCAATGCAGAGTCACAG
CGACGACACAGAGAAGCATATGAGGAAGATGATGAGCATTATCATCGTGGACCTCGTGTT
CAACAATGTGCTACATCGTAAATATATAAGAGTCGTAGAATTATTTAACCATCGTTTCTC
GCAACAAACCCGGAAATGAAGTTCTTTAAATTTAAAATTGATTCGTATATATGAAGGAAA
AATGCAATTTACCATCCAGCAAGAAAAAGCATAATAATAACTTATTTCATTCTATTCATA
TGTATTGCATTTTCAAATCACTCATATTTTGTTTTCTCACTCTCACTATATTTTATATGC
ATAATAATAATGTCCTTATTTTCTCTAAGTATGTGTTGAGATGAACGGAAAAATAAATAG
ATGAGGATTAAACTGTTAATGTAAAATTATAATACATAGAAATTACATGCTAGCAATGAA
AATAATCACATACCGTAGAATTTTTATGTTGAACTCATTTTTTTTTGTAACGTTAACAGA
TATAAATTCACATGCGTCTATGTTGATTATTAGCTTAACAATTAAAATTTCCTTTGACGT
CTATAAGTTAAAATAGATTATTTGAATTTCTTATTTTTAAGTTCATTCCTAAATTTAAAC
AGAAACAATACACAATATTCTAATAAAGATTATAGAAAATTAATTTAATGGTTTTTCTT
>g553.t12 Gene=g553 Length=353
MAYEVLSDPEKRQIYDEGGESAIKKGAGGGGGGFHSPMDLFDMFFGGGFGGGRQRERKGK
DLVHQMQVSLEEIYNGAVRKLALQKNVICEKCEGRGGKKGAVETCGTCQGKGVEVKIQQI
MPGFVQKHEQICRACQGQGEIINAKDRCKTCNGKKTVRDRKILEVHIEKGMQDGQRIVFN
GEGDQEPDLQPGDIIIVLDVKKHPVFQFSNGTDLAMVMDLQLVEALCGFQKVIKTLDQRD
LVITSLPGEVIKDNEIKCVMGEGMPEYKNPFEKGRLIIQFNVVFPNAIPPEYIPTLERCL
PSRPQVDIPITAEECMLSNYDPNAESQRRHREAYEEDDEHYHRGPRVQQCATS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g553.t12 | CDD | cd10747 | DnaJ_C | 60 | 285 | 1.17503E-41 |
| 15 | g553.t12 | CDD | cd10719 | DnaJ_zf | 89 | 155 | 1.11733E-19 |
| 12 | g553.t12 | Gene3D | G3DSA:1.10.287.110 | - | 1 | 55 | 2.7E-8 |
| 11 | g553.t12 | Gene3D | G3DSA:2.10.230.10 | - | 91 | 155 | 1.5E-20 |
| 13 | g553.t12 | Gene3D | G3DSA:2.60.260.20 | Urease metallochaperone UreE | 208 | 286 | 1.8E-21 |
| 10 | g553.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 321 | 353 | - |
| 9 | g553.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 324 | 345 | - |
| 3 | g553.t12 | PANTHER | PTHR43888 | DNAJ-LIKE-2, ISOFORM A-RELATED | 2 | 348 | 8.6E-147 |
| 4 | g553.t12 | PANTHER | PTHR43888:SF9 | DNAJ HOMOLOG SUBFAMILY A MEMBER 4 | 2 | 348 | 8.6E-147 |
| 1 | g553.t12 | Pfam | PF01556 | DnaJ C terminal domain | 63 | 285 | 2.6E-40 |
| 2 | g553.t12 | Pfam | PF00684 | DnaJ central domain | 89 | 155 | 2.3E-15 |
| 14 | g553.t12 | ProSiteProfiles | PS51188 | Zinc finger CR-type profile. | 76 | 160 | 23.622 |
| 8 | g553.t12 | SUPERFAMILY | SSF46565 | Chaperone J-domain | 2 | 53 | 4.71E-9 |
| 7 | g553.t12 | SUPERFAMILY | SSF49493 | HSP40/DnaJ peptide-binding domain | 61 | 204 | 7.85E-19 |
| 5 | g553.t12 | SUPERFAMILY | SSF57938 | DnaJ/Hsp40 cysteine-rich domain | 86 | 158 | 1.23E-17 |
| 6 | g553.t12 | 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.t12; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g553.t12.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.
