General information for g553.t13
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.t13 | TTS | g553.t13 | 4028265 | 4028265 |
| chr_3 | g553 | g553.t13 | isoform | g553.t13 | 4028467 | 4030708 |
| chr_3 | g553 | g553.t13 | exon | g553.t13.exon1 | 4028467 | 4029728 |
| chr_3 | g553 | g553.t13 | cds | g553.t13.CDS1 | 4028825 | 4029526 |
| chr_3 | g553 | g553.t13 | exon | g553.t13.exon2 | 4030232 | 4030418 |
| chr_3 | g553 | g553.t13 | exon | g553.t13.exon3 | 4030508 | 4030584 |
| chr_3 | g553 | g553.t13 | exon | g553.t13.exon4 | 4030675 | 4030708 |
| chr_3 | g553 | g553.t13 | TSS | g553.t13 | 4030963 | 4030963 |
Sequences
>g553.t13 Gene=g553 Length=1560
ATGGTGAAAGAAACAGGATATTATGATATTTTAGGCGTAAAGCCAAACTGCTCAAATGAT
GACCTCAAGAAGGCCTACAGAAAGCTTGCATTGAAATATCATCCAGACAAAAATCCTAAT
GAAGGTGAAAAGTTCAAACAGATCTCAATGGCTTATGAAGTCCTCTCTGATCCAGAAAAA
CGACAAATTTATGACGAAGGTGGCGAGTCTGCGATCAAAAAAGGAGCTGGAGGTGGTGGC
GGCGGTTTCCACAGTCCTATGGATCTTTTCGATATGTTCTTTGGAGGCGGATTTGGTGAC
AACGCGAACGTAAAGGAAAAGATTTGGTTCACCAAATGCAAGTGTCGTTGGAAGAAATAT
ACAATGGAGCTGTACGCAAATTGGCTCTTCAAAAGAATGTCATTTGCGAGAAATGTGAAG
GTCGTGGTGGAAAGAAAGGAGCTGTTGAAACTTGCGGCACTTGTCAAGGCAAAGGTGTTG
AAGTGAAAATTCAGCAAATCATGCCTGGATTTGTTCAAAAACATGAGCAAATTTGCCGGG
CATGTCAAGGACAAGGAGAAATCATCAATGCAAAAGACCGTTGCAAGACTTGTAATGGCA
AAAAGACAGTGCGTGATAGGAAAATTCTCGAAGTTCATATTGAAAAGGGAATGCAAGATG
GTCAGAGAATAGTCTTCAACGGTGAAGGTGATCAAGAACCCGATTTACAACCAGGCGATA
TCATTATCGTTTTGGATGTGAAAAAGCATCCAGTTTTCCAATTTAGCAATGGAACTGATC
TTGCAATGGTTATGGATCTGCAATTGGTTGAAGCACTCTGCGGTTTTCAGAAAGTCATCA
AGACACTTGATCAACGTGATTTAGTGATTACTAGCCTTCCAGGTGAAGTAATTAAAGACA
ATGAAATCAAGTGTGTGATGGGCGAGGGTATGCCAGAATACAAAAATCCATTCGAGAAAG
GTCGTTTGATTATTCAGTTTAATGTTGTATTTCCAAATGCAATTCCTCCTGAGTATATTC
CTACTCTTGAACGATGCTTACCTTCACGACCACAAGTTGACATACCCATCACTGCTGAAG
AATGTATGCTTTCAAATTACGATCCCAATGCAGAGTCACAGCGACGACACAGAGAAGCAT
ATGAGGAAGATGATGAGCATTATCATCGTGGACCTCGTGTTCAACAATGTGCTACATCGT
AAATATATAAGAGTCGTAGAATTATTTAACCATCGTTTCTCGCAACAAACCCGGAAATGA
AGTTCTTTAAATTTAAAATTGATTCGTATATATGAAGGAAAAATGCAATTTACCATCCAG
CAAGAAAAAGCATAATAATAACTTATTTCATTCTATTCATATGTATTGCATTTTCAAATC
ACTCATATTTTGTTTTCTCACTCTCACTATATTTTATATGCATAATAATAATGTCCTTAT
TTTCTCTAAGTATGTGTTGAGATGAACGGAAAAATAAATAGATGAGGATTAAACTGTTAA
TGTAAAATTATAATACATAGAAATTACATGCTAGCAATGAAAATAATCACATACCGTAGA
>g553.t13 Gene=g553 Length=233
MPGFVQKHEQICRACQGQGEIINAKDRCKTCNGKKTVRDRKILEVHIEKGMQDGQRIVFN
GEGDQEPDLQPGDIIIVLDVKKHPVFQFSNGTDLAMVMDLQLVEALCGFQKVIKTLDQRD
LVITSLPGEVIKDNEIKCVMGEGMPEYKNPFEKGRLIIQFNVVFPNAIPPEYIPTLERCL
PSRPQVDIPITAEECMLSNYDPNAESQRRHREAYEEDDEHYHRGPRVQQCATS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g553.t13 | CDD | cd10747 | DnaJ_C | 34 | 165 | 4.09475E-41 |
| 10 | g553.t13 | Gene3D | G3DSA:2.60.260.20 | Urease metallochaperone UreE | 8 | 81 | 2.8E-22 |
| 9 | g553.t13 | Gene3D | G3DSA:2.60.260.20 | Urease metallochaperone UreE | 88 | 166 | 8.2E-22 |
| 8 | g553.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 201 | 233 | - |
| 7 | g553.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 204 | 225 | - |
| 2 | g553.t13 | PANTHER | PTHR43888 | DNAJ-LIKE-2, ISOFORM A-RELATED | 2 | 228 | 8.0E-86 |
| 3 | g553.t13 | PANTHER | PTHR43888:SF9 | DNAJ HOMOLOG SUBFAMILY A MEMBER 4 | 2 | 228 | 8.0E-86 |
| 1 | g553.t13 | Pfam | PF01556 | DnaJ C terminal domain | 30 | 165 | 2.4E-34 |
| 4 | g553.t13 | SUPERFAMILY | SSF57938 | DnaJ/Hsp40 cysteine-rich domain | 5 | 38 | 1.44E-7 |
| 5 | g553.t13 | SUPERFAMILY | SSF49493 | HSP40/DnaJ peptide-binding domain | 27 | 87 | 1.06E-13 |
| 6 | g553.t13 | SUPERFAMILY | SSF49493 | HSP40/DnaJ peptide-binding domain | 90 | 170 | 8.76E-16 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g553/g553.t13; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g553.t13.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.
