General information for g5926.t4
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.t4 | isoform | g5926.t4 | 12878379 | 12879861 |
| chr_2 | g5926 | g5926.t4 | exon | g5926.t4.exon1 | 12878379 | 12879221 |
| chr_2 | g5926 | g5926.t4 | TTS | g5926.t4 | 12878406 | 12878406 |
| chr_2 | g5926 | g5926.t4 | cds | g5926.t4.CDS1 | 12878909 | 12879221 |
| chr_2 | g5926 | g5926.t4 | exon | g5926.t4.exon2 | 12879294 | 12879653 |
| chr_2 | g5926 | g5926.t4 | cds | g5926.t4.CDS2 | 12879294 | 12879653 |
| chr_2 | g5926 | g5926.t4 | exon | g5926.t4.exon3 | 12879723 | 12879861 |
| chr_2 | g5926 | g5926.t4 | cds | g5926.t4.CDS3 | 12879723 | 12879814 |
| chr_2 | g5926 | g5926.t4 | TSS | g5926.t4 | 12880474 | 12880474 |
Sequences
>g5926.t4 Gene=g5926 Length=1342
GTAGCAACATTCCTAATAATTATTTTAATGCTTTCTATGGTAATACAATGGACGCTAATA
ATATTTTGGCTCAACAATATGCAATGCAAACATGGATGCAACAAGCTTATGCTCAGTATA
TGAGTCAATATATGAATATTATGTCACAATCAGAGCAACAAGCTAATGCTCAAACAACAA
ATTTTGCTTTTATGCAGCCTCCAATGCCTTCTATACCAACTCCAACTACAGTGACTCCAT
CAACACAATCGCCAAATGCTGAAACTCAAGCAGCATCTGCAACTCCTGTAGCGGAACAAC
AACAAGCACAACAGAATCAACCTGCAGCCGAGCCACAACGTCGATTTCCAAACATCATTC
AAGATGAGCAGGAAAATCGTGATTGGCTTGATATTCTTTATTCAATGTCTCGTCTTATGA
TACTTTTGTGTCTTGTCTATTTTTATTCGTCGCCTCTTAGATGTCTCATTGTAATTCTCA
TAGGTGTATCAATTTATTTATATCACATTTACAAACAAAATCAAAATCGTCTTAATAACA
ATAATACAAATCGTGTTAATTTAAATGTAAATAACAATCAACCAGCTGCTGCTGCACCAC
AACAACCAGCACCAGAAAATAATGAAAATCCTGAACAAAATAATGAGAGTCAATCAAATC
AGTCATCACTTTCTGAAAGTATTAGTGAAAGTGAGCCTTTAGTGAATGAAATTTCTCAAA
ACGAAGAACCACCAGTTTCAATGTTGACAGTGTTAAGAACTTTTGTTATATCATTTGTAG
CTTCAATTATTCCAGAGCATCCCGCAATGTGAGAGAATTTCATATTGTTTATGGGCATTT
ATTTGGTAGTTTACATAATTATATCTATTTTTAAAATAGTTAGAGAAGCAAATGTTCTTG
ACTAACTCCACTGAGGGATTGAAAACACCGTATATTTGTTATTGATTAAACTTTCGCACT
GAGACTAATGAACTAATCGTTTGTTCACCTCAATTGTTCCTTTATTTAGTGTGCTGACAA
AAAAATTAAAGTGGTATTGCAGCGGTAACTATTGTTATAAAAAATTATATTTTTATTTAG
TTCATTAACACTAAATGAATGAAAGAAAAATATGAAAATATTCTTTCAATATTAATTATT
TATTTATGAGAATGTACCTTTAATCCCTTGGCTTCAAACACACATCCGTGTTTAAAAGTT
TTAATTTAAGTTTTAAAAAACTGTGTTAGATAAAATACAAAATAAATCTTGTAACAACTT
CCTTATCATAGATAAAAGAGGAATAAAAAAAAAGTTTTATTGATGCATAATAAAAATTGT
GAATTTATTTAAATTGAAAAAT
>g5926.t4 Gene=g5926 Length=254
MDANNILAQQYAMQTWMQQAYAQYMSQYMNIMSQSEQQANAQTTNFAFMQPPMPSIPTPT
TVTPSTQSPNAETQAASATPVAEQQQAQQNQPAAEPQRRFPNIIQDEQENRDWLDILYSM
SRLMILLCLVYFYSSPLRCLIVILIGVSIYLYHIYKQNQNRLNNNNTNRVNLNVNNNQPA
AAAPQQPAPENNENPEQNNESQSNQSSLSESISESEPLVNEISQNEEPPVSMLTVLRTFV
ISFVASIIPEHPAM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5926.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 59 | 104 | - |
| 4 | g5926.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 60 | 96 | - |
| 5 | g5926.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 179 | 224 | - |
| 1 | g5926.t4 | PANTHER | PTHR12943:SF27 | HOMOCYSTEINE-INDUCED ENDOPLASMIC RETICULUM PROTEIN, ISOFORM A | 9 | 253 | 1.4E-30 |
| 2 | g5926.t4 | PANTHER | PTHR12943 | HOMOCYSTEINE-RESPONSIVE ENDOPLASMIC RETICULUM-RESIDENT UNIQUITIN-LIKE DOMAIN HERPUD PROTEIN FAMILY MEMBER | 9 | 253 | 1.4E-30 |
| 8 | g5926.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 112 | - |
| 11 | g5926.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 113 | 133 | - |
| 9 | g5926.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 134 | 138 | - |
| 10 | g5926.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 139 | 155 | - |
| 7 | g5926.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 156 | 254 | - |
| 3 | g5926.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 130 | 152 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5926/g5926.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5926.t4.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.
