General information for g5606.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5606 is located on chr_2: 10587633..10588371 (- 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 | g5606 | g5606.t1 | TTS | g5606.t1 | 10587367 | 10587367 |
| chr_2 | g5606 | g5606.t1 | isoform | g5606.t1 | 10587633 | 10588371 |
| chr_2 | g5606 | g5606.t1 | exon | g5606.t1.exon1 | 10587633 | 10587853 |
| chr_2 | g5606 | g5606.t1 | cds | g5606.t1.CDS1 | 10587633 | 10587853 |
| chr_2 | g5606 | g5606.t1 | exon | g5606.t1.exon2 | 10587920 | 10588243 |
| chr_2 | g5606 | g5606.t1 | cds | g5606.t1.CDS2 | 10587920 | 10588243 |
| chr_2 | g5606 | g5606.t1 | exon | g5606.t1.exon3 | 10588362 | 10588371 |
| chr_2 | g5606 | g5606.t1 | cds | g5606.t1.CDS3 | 10588362 | 10588371 |
| chr_2 | g5606 | g5606.t1 | TSS | g5606.t1 | 10588400 | 10588400 |
Sequences
>g5606.t1 Gene=g5606 Length=555
ATGTCTGGAGAGCCAACAGCACCACCGTTGACACCTCAAAATATGGGATTCATTGTTCAA
CAACAACCACATTTTCCTATTCCGCCACCACCATATCCAACGAATTTTACGAATGATCCT
TCATCAAATTCACTGCCCTATCCAGGATCGAATTCACTGCCTTATCCTCAATCGAATTCA
CTACCCTATCCTCCATCGGATGCACTGCCTTATCCTTCATCAAATTCTTTGCCATATCCT
TCATTTAATCCACAATCAACAGACGTCCAAACAACTCAACCAACAGCCAATACAACAAAT
ACGATTATAGTTCAACCACCACAGCTTGGATCTGATCCAGTCGTATGTTACTGTCCAAAC
TGTAATGAGAATGTGACTACAAAAGTCGATTATAAAGCTGGCACTCAAACACACTTGTCT
GCTGCTCTTCTTTGTGCATTAAATGATGATTGTTGTTGTGCCTTGCTTCCATATTGCTGC
AATTGTACTAAAGATGCTCACCATTATTGCCCAAAGTGTAATCACTATTTTGGAAAAAGT
CAACCATTTGGTTAA
>g5606.t1 Gene=g5606 Length=184
MSGEPTAPPLTPQNMGFIVQQQPHFPIPPPPYPTNFTNDPSSNSLPYPGSNSLPYPQSNS
LPYPPSDALPYPSSNSLPYPSFNPQSTDVQTTQPTANTTNTIIVQPPQLGSDPVVCYCPN
CNENVTTKVDYKAGTQTHLSAALLCALNDDCCCALLPYCCNCTKDAHHYCPKCNHYFGKS
QPFG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5606.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 6 | g5606.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 50 | - |
| 2 | g5606.t1 | PANTHER | PTHR23292:SF14 | FI16615P1-RELATED | 53 | 178 | 4.9E-24 |
| 3 | g5606.t1 | PANTHER | PTHR23292 | LIPOPOLYSACCHARIDE-INDUCED TUMOR NECROSIS FACTOR-ALPHA FACTOR | 53 | 178 | 4.9E-24 |
| 1 | g5606.t1 | Pfam | PF10601 | LITAF-like zinc ribbon domain | 112 | 179 | 1.2E-19 |
| 7 | g5606.t1 | ProSiteProfiles | PS51837 | LITAF domain profile. | 98 | 182 | 17.796 |
| 4 | g5606.t1 | SMART | SM00714 | litaf | 113 | 182 | 1.8E-12 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5606/g5606.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5606.t1.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. There were no conditions that were differentially expressed