General information for g5504.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5504 is located on chr_2: 9952421..9953822 (+ 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 | g5504 | g5504.t1 | isoform | g5504.t1 | 9939495 | 9952421 |
| chr_2 | g5504 | g5504.t1 | exon | g5504.t1.exon1 | 9939495 | 9939591 |
| chr_2 | g5504 | g5504.t1 | cds | g5504.t1.CDS1 | 9939495 | 9939591 |
| chr_2 | g5504 | g5504.t1 | exon | g5504.t1.exon2 | 9947352 | 9947481 |
| chr_2 | g5504 | g5504.t1 | cds | g5504.t1.CDS2 | 9947352 | 9947481 |
| chr_2 | g5504 | g5504.t1 | exon | g5504.t1.exon3 | 9947988 | 9948105 |
| chr_2 | g5504 | g5504.t1 | cds | g5504.t1.CDS3 | 9947988 | 9948105 |
| chr_2 | g5504 | g5504.t1 | exon | g5504.t1.exon4 | 9949181 | 9949274 |
| chr_2 | g5504 | g5504.t1 | cds | g5504.t1.CDS4 | 9949181 | 9949274 |
| chr_2 | g5504 | g5504.t1 | exon | g5504.t1.exon5 | 9950877 | 9950990 |
| chr_2 | g5504 | g5504.t1 | cds | g5504.t1.CDS5 | 9950877 | 9950990 |
| chr_2 | g5504 | g5504.t1 | exon | g5504.t1.exon6 | 9952204 | 9952421 |
| chr_2 | g5504 | g5504.t1 | cds | g5504.t1.CDS6 | 9952204 | 9952421 |
| chr_2 | g5504 | g5504.t1 | TSS | g5504.t1 | NA | NA |
| chr_2 | g5504 | g5504.t1 | TTS | g5504.t1 | NA | NA |
Sequences
>g5504.t1 Gene=g5504 Length=771
ATGAAATTTAATGAATATTTAAGTGTTTTGGTCTACAAACTTGTTCTAGTCATAAACTTG
ATTAATGGCAAAATGCTGAATGAAAGGGATAAGAATGCACAAATTGTCGATGTGATAGCT
GTCGAGGGAAAAAGCGCACAGCTTCCATGTCCAATGAGTGCGCCATTGAGCGAAGTATCC
ATGTTATTTTTCTTTAAATCAGCACATGGAGGAATACCTCTCTATAGTGTTGATGTGCGA
GATAAAAATTCACAGCAACGTCCGAAGCATTGGTCAGCGCCTGAAGTCTTCGGATCACGT
GCCAACTTTTCCATTGACAATAAACCTGAATCGTTAGTAATTAAGGATATCAAACGACAT
GATCAAGGAGTTTATCGTTGTCGAATAGACTTTCGAACGAGTCAAACGCAAAGCTACACA
TACAATTTATCAGTTATAATTTTACCTGAATCGCCTGTTGTGCTTGATAGATGGGGAAGA
CAACTGAATAGCACAAAAATTGGTCCAGTGCAGGAGGGAGAAGACATTATATTGTCATGT
CGCGTAGTTGGAGGACGCCCACAGCCGACAGTGCGATGGCTCATAAATGGACTGCCCGTT
GATGATCAATATGAACACAACTCAGGCGATGTGATTGAAAATAGACTCCTATGGCCTCAA
ATACAAAGGAACGATCTCAATTCAATATTCACCTGTCAAGCGTCAAATACTAAACTTGTG
GAGCCTAAGGAAACATCTTTTGTGTTGGATATGCACTGTAAGTTATCATGA
>g5504.t1 Gene=g5504 Length=256
MKFNEYLSVLVYKLVLVINLINGKMLNERDKNAQIVDVIAVEGKSAQLPCPMSAPLSEVS
MLFFFKSAHGGIPLYSVDVRDKNSQQRPKHWSAPEVFGSRANFSIDNKPESLVIKDIKRH
DQGVYRCRIDFRTSQTQSYTYNLSVIILPESPVVLDRWGRQLNSTKIGPVQEGEDIILSC
RVVGGRPQPTVRWLINGLPVDDQYEHNSGDVIENRLLWPQIQRNDLNSIFTCQASNTKLV
EPKETSFVLDMHCKLS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5504.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 27 | 152 | 6.7E-16 |
| 10 | g5504.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 153 | 252 | 3.0E-16 |
| 3 | g5504.t1 | PANTHER | PTHR23278 | SIDESTEP PROTEIN | 28 | 254 | 6.1E-68 |
| 1 | g5504.t1 | Pfam | PF07686 | Immunoglobulin V-set domain | 38 | 145 | 9.2E-7 |
| 2 | g5504.t1 | Pfam | PF13927 | Immunoglobulin domain | 166 | 236 | 3.4E-10 |
| 15 | g5504.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 16 | g5504.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 22 | - |
| 14 | g5504.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 23 | 256 | - |
| 12 | g5504.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 42 | 144 | 6.851 |
| 13 | g5504.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 149 | 246 | 10.353 |
| 6 | g5504.t1 | SMART | SM00409 | IG_3c | 35 | 146 | 8.4E-5 |
| 9 | g5504.t1 | SMART | SM00408 | igc2_5 | 41 | 134 | 0.17 |
| 7 | g5504.t1 | SMART | SM00409 | IG_3c | 165 | 252 | 8.2 |
| 8 | g5504.t1 | SMART | SM00408 | igc2_5 | 171 | 239 | 0.042 |
| 4 | g5504.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 36 | 153 | 5.14E-12 |
| 5 | g5504.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 167 | 252 | 1.22E-13 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5504/g5504.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5504.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