General information for g5926.t3
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.t3 | isoform | g5926.t3 | 12878379 | 12879861 |
| chr_2 | g5926 | g5926.t3 | exon | g5926.t3.exon1 | 12878379 | 12878841 |
| chr_2 | g5926 | g5926.t3 | TTS | g5926.t3 | 12878406 | 12878406 |
| chr_2 | g5926 | g5926.t3 | exon | g5926.t3.exon2 | 12878913 | 12879221 |
| chr_2 | g5926 | g5926.t3 | exon | g5926.t3.exon3 | 12879290 | 12879653 |
| chr_2 | g5926 | g5926.t3 | cds | g5926.t3.CDS1 | 12879290 | 12879653 |
| chr_2 | g5926 | g5926.t3 | exon | g5926.t3.exon4 | 12879723 | 12879861 |
| chr_2 | g5926 | g5926.t3 | cds | g5926.t3.CDS2 | 12879723 | 12879814 |
| chr_2 | g5926 | g5926.t3 | TSS | g5926.t3 | 12880474 | 12880474 |
Sequences
>g5926.t3 Gene=g5926 Length=1275
GTAGCAACATTCCTAATAATTATTTTAATGCTTTCTATGGTAATACAATGGACGCTAATA
ATATTTTGGCTCAACAATATGCAATGCAAACATGGATGCAACAAGCTTATGCTCAGTATA
TGAGTCAATATATGAATATTATGTCACAATCAGAGCAACAAGCTAATGCTCAAACAACAA
ATTTTGCTTTTATGCAGCCTCCAATGCCTTCTATACCAACTCCAACTACAGTGACTCCAT
CAACACAATCGCCAAATGCTGAAACTCAAGCAGCATCTGCAACTCCTGTAGCGGAACAAC
AACAAGCACAACAGAATCAACCTGCAGCCGAGCCACAACGTCGATTTCCAAACATCATTC
AAGATGAGCAGGAAAATCGTGATTGGCTTGATATTCTTTATTCAATGTCTCGTCTTATGA
TACTTTTGTGTCTTGTCTATTTTTATTCGTCGCCTCTTAGATGTCTCATTGTAATTCTCA
TAGGTGTATCAATTTATTTGTAAATATCACATTTACAAACAAAATCAAAATCGTCTTAAT
AACAATAATACAAATCGTGTTAATTTAAATGTAAATAACAATCAACCAGCTGCTGCTGCA
CCACAACAACCAGCACCAGAAAATAATGAAAATCCTGAACAAAATAATGAGAGTCAATCA
AATCAGTCATCACTTTCTGAAAGTATTAGTGAAAGTGAGCCTTTAGTGAATGAAATTTCT
CAAAACGAAGAACCACCAGTTTCAATGTTGACAGTGTTAAGAACTTTTGTTATATCATTT
GTAGCTTCAATTATTCCAGAGCATCCCGCAATTTAGAGAAGCAAATGTTCTTGACTAACT
CCACTGAGGGATTGAAAACACCGTATATTTGTTATTGATTAAACTTTCGCACTGAGACTA
ATGAACTAATCGTTTGTTCACCTCAATTGTTCCTTTATTTAGTGTGCTGACAAAAAAATT
AAAGTGGTATTGCAGCGGTAACTATTGTTATAAAAAATTATATTTTTATTTAGTTCATTA
ACACTAAATGAATGAAAGAAAAATATGAAAATATTCTTTCAATATTAATTATTTATTTAT
GAGAATGTACCTTTAATCCCTTGGCTTCAAACACACATCCGTGTTTAAAAGTTTTAATTT
AAGTTTTAAAAAACTGTGTTAGATAAAATACAAAATAAATCTTGTAACAACTTCCTTATC
ATAGATAAAAGAGGAATAAAAAAAAAGTTTTATTGATGCATAATAAAAATTGTGAATTTA
TTTAAATTGAAAAAT
>g5926.t3 Gene=g5926 Length=151
MDANNILAQQYAMQTWMQQAYAQYMSQYMNIMSQSEQQANAQTTNFAFMQPPMPSIPTPT
TVTPSTQSPNAETQAASATPVAEQQQAQQNQPAAEPQRRFPNIIQDEQENRDWLDILYSM
SRLMILLCLVYFYSSPLRCLIVILIGVSIYL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5926.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 52 | 103 | - |
| 4 | g5926.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 60 | 96 | - |
| 1 | g5926.t3 | PANTHER | PTHR12943:SF27 | HOMOCYSTEINE-INDUCED ENDOPLASMIC RETICULUM PROTEIN, ISOFORM A | 9 | 151 | 1.6E-17 |
| 2 | g5926.t3 | PANTHER | PTHR12943 | HOMOCYSTEINE-RESPONSIVE ENDOPLASMIC RETICULUM-RESIDENT UNIQUITIN-LIKE DOMAIN HERPUD PROTEIN FAMILY MEMBER | 9 | 151 | 1.6E-17 |
| 6 | g5926.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 122 | - |
| 8 | g5926.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 123 | 150 | - |
| 7 | g5926.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 151 | 151 | - |
| 3 | g5926.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 147 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5926/g5926.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5926.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
