General information for g553.t9
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.t9 | isoform | g553.t9 | 4028247 | 4030935 |
| chr_3 | g553 | g553.t9 | exon | g553.t9.exon1 | 4028247 | 4029728 |
| chr_3 | g553 | g553.t9 | TTS | g553.t9 | 4028265 | 4028265 |
| chr_3 | g553 | g553.t9 | cds | g553.t9.CDS1 | 4028825 | 4029728 |
| chr_3 | g553 | g553.t9 | exon | g553.t9.exon2 | 4030225 | 4030418 |
| chr_3 | g553 | g553.t9 | cds | g553.t9.CDS2 | 4030225 | 4030418 |
| chr_3 | g553 | g553.t9 | exon | g553.t9.exon3 | 4030508 | 4030584 |
| chr_3 | g553 | g553.t9 | cds | g553.t9.CDS3 | 4030508 | 4030584 |
| chr_3 | g553 | g553.t9 | exon | g553.t9.exon4 | 4030675 | 4030727 |
| chr_3 | g553 | g553.t9 | cds | g553.t9.CDS4 | 4030675 | 4030708 |
| chr_3 | g553 | g553.t9 | exon | g553.t9.exon5 | 4030887 | 4030935 |
| chr_3 | g553 | g553.t9 | TSS | g553.t9 | 4030963 | 4030963 |
Sequences
>g553.t9 Gene=g553 Length=1855
TTTTAAGTAAAACTTGAACAGTTTCAGACGTTTTTGCGAGAGAAAAAGGTTAATATAATT
CTACAAACATGGTGAAAGAAACAGGATATTATGATATTTTAGGCGTAAAGCCAAACTGCT
CAAATGATGACCTCAAGAAGGCCTACAGAAAGCTTGCATTGAAATATCATCCAGACAAAA
ATCCTAATGAAGGTGAAAAGTTCAAACAGATCTCAATGGCTTATGAAGTCCTCTCTGATC
CAGAAAAACGACAAATTTATGACGAAGGTGGCGAGTCTGCGATCAAAAAAGGAGCTGGAG
GTGGTGGCGGCGGTTTCCACAGTCCTATGGATCTTTTCGATATGTTCTTTGGAGGCGGAT
TTGGTGGTGGCAGACAACGCGAACGTAAAGGAAAAGATTTGGTTCACCAAATGCAAGTGT
CGTTGGAAGAAATATACAATGGAGCTGTACGCAAATTGGCTCTTCAAAAGAATGTCATTT
GCGAGAAATGTGAAGGTCGTGGTGGAAAGAAAGGAGCTGTTGAAACTTGCGGCACTTGTC
AAGGCAAAGGTGTTGAAGTGAAAATTCAGCAAATCATGCCTGGATTTGTTCAAAAACATG
AGCAAATTTGCCGGGCATGTCAAGGACAAGGAGAAATCATCAATGCAAAAGACCGTTGCA
AGACTTGTAATGGCAAAAAGACAGTGCGTGATAGGAAAATTCTCGAAGTTCATATTGAAA
AGGGAATGCAAGATGGTCAGAGAATAGTCTTCAACGGTGAAGGTGATCAAGAACCCGATT
TACAACCAGGCGATATCATTATCGTTTTGGATGTGAAAAAGCATCCAGTTTTCCAATTTA
GCAATGGAACTGATCTTGCAATGGTTATGGATCTGCAATTGGTTGAAGCACTCTGCGGTT
TTCAGAAAGTCATCAAGACACTTGATCAACGTGATTTAGTGATTACTAGCCTTCCAGGTG
AAGTAATTAAAGACAATGAAATCAAGTGTGTGATGGGCGAGGGTATGCCAGAATACAAAA
ATCCATTCGAGAAAGGTCGTTTGATTATTCAGTTTAATGTTGTATTTCCAAATGCAATTC
CTCCTGAGTATATTCCTACTCTTGAACGATGCTTACCTTCACGACCACAAGTTGACATAC
CCATCACTGCTGAAGAATGTATGCTTTCAAATTACGATCCCAATGCAGAGTCACAGCGAC
GACACAGAGAAGCATATGAGGAAGATGATGAGCATTATCATCGTGGACCTCGTGTTCAAC
AATGTGCTACATCGTAAATATATAAGAGTCGTAGAATTATTTAACCATCGTTTCTCGCAA
CAAACCCGGAAATGAAGTTCTTTAAATTTAAAATTGATTCGTATATATGAAGGAAAAATG
CAATTTACCATCCAGCAAGAAAAAGCATAATAATAACTTATTTCATTCTATTCATATGTA
TTGCATTTTCAAATCACTCATATTTTGTTTTCTCACTCTCACTATATTTTATATGCATAA
TAATAATGTCCTTATTTTCTCTAAGTATGTGTTGAGATGAACGGAAAAATAAATAGATGA
GGATTAAACTGTTAATGTAAAATTATAATACATAGAAATTACATGCTAGCAATGAAAATA
ATCACATACCGTAGAATTTTTATGTTGAACTCATTTTTTTTTGTAACGTTAACAGATATA
AATTCACATGCGTCTATGTTGATTATTAGCTTAACAATTAAAATTTCCTTTGACGTCTAT
AAGTTAAAATAGATTATTTGAATTTCTTATTTTTAAGTTCATTCCTAAATTTAAACAGAA
ACAATACACAATATTCTAATAAAGATTATAGAAAATTAATTTAATGGTTTTTCTT
>g553.t9 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.t9 | CDD | cd06257 | DnaJ | 7 | 57 | 2.27234E-24 |
| 19 | g553.t9 | CDD | cd10747 | DnaJ_C | 109 | 334 | 1.95035E-41 |
| 18 | g553.t9 | CDD | cd10719 | DnaJ_zf | 138 | 204 | 4.93255E-20 |
| 15 | g553.t9 | Gene3D | G3DSA:1.10.287.110 | - | 3 | 104 | 6.0E-33 |
| 14 | g553.t9 | Gene3D | G3DSA:2.10.230.10 | - | 140 | 204 | 1.9E-20 |
| 16 | g553.t9 | Gene3D | G3DSA:2.60.260.20 | Urease metallochaperone UreE | 257 | 335 | 2.2E-21 |
| 6 | g553.t9 | Hamap | MF_01152 | Chaperone protein DnaJ [dnaJ]. | 3 | 382 | 26.86924 |
| 23 | g553.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 370 | 402 | - |
| 22 | g553.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 373 | 394 | - |
| 4 | g553.t9 | PANTHER | PTHR43888 | DNAJ-LIKE-2, ISOFORM A-RELATED | 1 | 397 | 6.3E-179 |
| 5 | g553.t9 | PANTHER | PTHR43888:SF9 | DNAJ HOMOLOG SUBFAMILY A MEMBER 4 | 1 | 397 | 6.3E-179 |
| 9 | g553.t9 | PRINTS | PR00625 | DnaJ domain signature | 8 | 26 | 1.4E-18 |
| 7 | g553.t9 | PRINTS | PR00625 | DnaJ domain signature | 26 | 41 | 1.4E-18 |
| 8 | g553.t9 | PRINTS | PR00625 | DnaJ domain signature | 60 | 79 | 1.4E-18 |
| 3 | g553.t9 | Pfam | PF00226 | DnaJ domain | 7 | 65 | 1.0E-26 |
| 1 | g553.t9 | Pfam | PF01556 | DnaJ C terminal domain | 112 | 334 | 3.8E-40 |
| 2 | g553.t9 | Pfam | PF00684 | DnaJ central domain | 138 | 204 | 2.8E-15 |
| 21 | g553.t9 | ProSitePatterns | PS00636 | Nt-dnaJ domain signature. | 45 | 64 | - |
| 25 | g553.t9 | ProSiteProfiles | PS50076 | dnaJ domain profile. | 6 | 68 | 22.989 |
| 24 | g553.t9 | ProSiteProfiles | PS51188 | Zinc finger CR-type profile. | 125 | 209 | 23.622 |
| 20 | g553.t9 | SMART | SM00271 | dnaj_3 | 5 | 60 | 2.7E-29 |
| 13 | g553.t9 | SUPERFAMILY | SSF46565 | Chaperone J-domain | 2 | 102 | 2.88E-36 |
| 11 | g553.t9 | SUPERFAMILY | SSF49493 | HSP40/DnaJ peptide-binding domain | 104 | 256 | 7.46E-19 |
| 10 | g553.t9 | SUPERFAMILY | SSF57938 | DnaJ/Hsp40 cysteine-rich domain | 135 | 207 | 1.57E-17 |
| 12 | g553.t9 | 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.t9; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g553.t9.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
- This transcript has been annotated with K09502 (DnaJ homolog subfamily A member 1)
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.
