General information for g5926.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5926 is located on chr_2: 12880705..12881875 (- 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_2 | g5926 | g5926.t1 | TTS | g5926.t1 | 12878406 | 12878406 |
| chr_2 | g5926 | g5926.t1 | isoform | g5926.t1 | 12878838 | 12881579 |
| chr_2 | g5926 | g5926.t1 | exon | g5926.t1.exon1 | 12878838 | 12878841 |
| chr_2 | g5926 | g5926.t1 | cds | g5926.t1.CDS1 | 12878838 | 12878841 |
| chr_2 | g5926 | g5926.t1 | exon | g5926.t1.exon2 | 12878913 | 12879221 |
| chr_2 | g5926 | g5926.t1 | cds | g5926.t1.CDS2 | 12878913 | 12879221 |
| chr_2 | g5926 | g5926.t1 | exon | g5926.t1.exon3 | 12879294 | 12879653 |
| chr_2 | g5926 | g5926.t1 | cds | g5926.t1.CDS3 | 12879294 | 12879653 |
| chr_2 | g5926 | g5926.t1 | exon | g5926.t1.exon4 | 12879723 | 12880168 |
| chr_2 | g5926 | g5926.t1 | cds | g5926.t1.CDS4 | 12879723 | 12880168 |
| chr_2 | g5926 | g5926.t1 | exon | g5926.t1.exon5 | 12881454 | 12881579 |
| chr_2 | g5926 | g5926.t1 | cds | g5926.t1.CDS5 | 12881454 | 12881579 |
| chr_2 | g5926 | g5926.t1 | TSS | g5926.t1 | 12881780 | 12881780 |
Sequences
>g5926.t1 Gene=g5926 Length=1245
ATGGACTCAGAAATGATTTTAAATCTCGTAATAAAAGTCCAGCAATTTGAGGACAAACGA
ATTGAGGCGAAAGCATCATGGAATATAAGAGAATTAAAAGGAAAACTTAGTGAAATATAT
CCTACAAGCACTGAAGAACAGAAACTTATATATTCTGGAAAGCTCTTGAACGATACTGTT
ATATTAAAGGACGTTTTACGAGAATACGAAGGACAAGAGGCTCATACAGTTCATTTAGTT
TTCACACCCAAACAAAATTCGCGTATTCAAAATAAATTTCAGGAAAGCAAACAAAATTCA
TCTGTCAACTCCATTAATAACCAGACATCATCATCGTCATCAGATATGAGTACAAGCGAA
TTAAGACAGAGACATACAGCTACTGCCACTGTTGCTCCTAACAATACAACTGAACAACAA
CAGATGACTTCTAGTAGCAACATTCCTAATAATTATTTTAATGCTTTCTATGGTAATACA
ATGGACGCTAATAATATTTTGGCTCAACAATATGCAATGCAAACATGGATGCAACAAGCT
TATGCTCAGTATATGAGTCAATATATGAATATTATGTCACAATCAGAGCAACAAGCTAAT
GCTCAAACAACAAATTTTGCTTTTATGCAGCCTCCAATGCCTTCTATACCAACTCCAACT
ACAGTGACTCCATCAACACAATCGCCAAATGCTGAAACTCAAGCAGCATCTGCAACTCCT
GTAGCGGAACAACAACAAGCACAACAGAATCAACCTGCAGCCGAGCCACAACGTCGATTT
CCAAACATCATTCAAGATGAGCAGGAAAATCGTGATTGGCTTGATATTCTTTATTCAATG
TCTCGTCTTATGATACTTTTGTGTCTTGTCTATTTTTATTCGTCGCCTCTTAGATGTCTC
ATTGTAATTCTCATAGGTGTATCAATTTATTTATATCACATTTACAAACAAAATCAAAAT
CGTCTTAATAACAATAATACAAATCGTGTTAATTTAAATGTAAATAACAATCAACCAGCT
GCTGCTGCACCACAACAACCAGCACCAGAAAATAATGAAAATCCTGAACAAAATAATGAG
AGTCAATCAAATCAGTCATCACTTTCTGAAAGTATTAGTGAAAGTGAGCCTTTAGTGAAT
GAAATTTCTCAAAACGAAGAACCACCAGTTTCAATGTTGACAGTGTTAAGAACTTTTGTT
ATATCATTTGTAGCTTCAATTATTCCAGAGCATCCCGCAATTTAG
>g5926.t1 Gene=g5926 Length=414
MDSEMILNLVIKVQQFEDKRIEAKASWNIRELKGKLSEIYPTSTEEQKLIYSGKLLNDTV
ILKDVLREYEGQEAHTVHLVFTPKQNSRIQNKFQESKQNSSVNSINNQTSSSSSDMSTSE
LRQRHTATATVAPNNTTEQQQMTSSSNIPNNYFNAFYGNTMDANNILAQQYAMQTWMQQA
YAQYMSQYMNIMSQSEQQANAQTTNFAFMQPPMPSIPTPTTVTPSTQSPNAETQAASATP
VAEQQQAQQNQPAAEPQRRFPNIIQDEQENRDWLDILYSMSRLMILLCLVYFYSSPLRCL
IVILIGVSIYLYHIYKQNQNRLNNNNTNRVNLNVNNNQPAAAAPQQPAPENNENPEQNNE
SQSNQSSLSESISESEPLVNEISQNEEPPVSMLTVLRTFVISFVASIIPEHPAI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5926.t1 | Gene3D | G3DSA:3.10.20.90 | - | 2 | 89 | 1.3E-16 |
| 13 | g5926.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 92 | 145 | - |
| 14 | g5926.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 219 | 264 | - |
| 16 | g5926.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 220 | 256 | - |
| 15 | g5926.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 339 | 384 | - |
| 2 | g5926.t1 | PANTHER | PTHR12943:SF27 | HOMOCYSTEINE-INDUCED ENDOPLASMIC RETICULUM PROTEIN, ISOFORM A | 9 | 413 | 5.5E-64 |
| 3 | g5926.t1 | PANTHER | PTHR12943 | HOMOCYSTEINE-RESPONSIVE ENDOPLASMIC RETICULUM-RESIDENT UNIQUITIN-LIKE DOMAIN HERPUD PROTEIN FAMILY MEMBER | 9 | 413 | 5.5E-64 |
| 1 | g5926.t1 | Pfam | PF00240 | Ubiquitin family | 11 | 83 | 7.8E-10 |
| 8 | g5926.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 272 | - |
| 10 | g5926.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 273 | 292 | - |
| 6 | g5926.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 293 | 298 | - |
| 9 | g5926.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 299 | 315 | - |
| 7 | g5926.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 316 | 414 | - |
| 17 | g5926.t1 | ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 7 | 86 | 14.164 |
| 12 | g5926.t1 | SMART | SM00213 | ubq_7 | 7 | 82 | 3.3E-8 |
| 4 | g5926.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 7 | 85 | 9.44E-14 |
| 11 | g5926.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 290 | 312 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5926/g5926.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5926.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | 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.
