General information for g11539.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nuclear protein localization protein 4-like protein.
Parent gene
- The parent gene g11539 is located on chr_1: 16931925..16932999 (+ 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_1 | g11539 | g11539.t1 | isoform | g11539.t1 | 16931308 | 16931925 |
| chr_1 | g11539 | g11539.t1 | exon | g11539.t1.exon1 | 16931308 | 16931499 |
| chr_1 | g11539 | g11539.t1 | cds | g11539.t1.CDS1 | 16931308 | 16931499 |
| chr_1 | g11539 | g11539.t1 | exon | g11539.t1.exon2 | 16931563 | 16931747 |
| chr_1 | g11539 | g11539.t1 | cds | g11539.t1.CDS2 | 16931563 | 16931747 |
| chr_1 | g11539 | g11539.t1 | exon | g11539.t1.exon3 | 16931808 | 16931925 |
| chr_1 | g11539 | g11539.t1 | cds | g11539.t1.CDS3 | 16931808 | 16931925 |
| chr_1 | g11539 | g11539.t1 | TTS | g11539.t1 | 16932008 | 16932008 |
| chr_1 | g11539 | g11539.t1 | TSS | g11539.t1 | NA | NA |
Sequences
>g11539.t1 Gene=g11539 Length=495
ATGGCACGTCCTCTACCAGTTGAATATCTCCTCGTCGATGTTCCAGCATCATCACCTTTA
GTTCCTCTTTTCACATTCCCATCACGACAACATCATTTTCCAATTGAAAATCGACTATTG
GATAATCATCTTCAAGACTTTGCAGCTTTTCACAATTACATGCAAATGTATGCAGCACGT
GATTTTCTATTGGCAATGTCAGATTTTCACGTTTTACTATATCTTTATGGTTTGACATGC
TTTGATATTAAAATGAAAAGTCAAATAGGCCCATTGCTACAGGCTGTACGAAATCAAGAT
TCGGCTCAAGCGAATCAATTTATGAGAGGTGAAGTCTGGCGAACATTTGAACAGCTGATC
AGCGCACACGTTCACGAGAATGATAATCATATGGTGCCGGAAAGAGTCGACACTAATAAT
TGGACCTGTAATCATTGCACTTTCATCAACAGTAAGGATCTACAGACTTGTGAAATGTGC
GGCTTACCTCGCTAA
>g11539.t1 Gene=g11539 Length=164
MARPLPVEYLLVDVPASSPLVPLFTFPSRQHHFPIENRLLDNHLQDFAAFHNYMQMYAAR
DFLLAMSDFHVLLYLYGLTCFDIKMKSQIGPLLQAVRNQDSAQANQFMRGEVWRTFEQLI
SAHVHENDNHMVPERVDTNNWTCNHCTFINSKDLQTCEMCGLPR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g11539.t1 | Gene3D | G3DSA:2.20.28.140 | - | 135 | 164 | 3.4E-7 |
| 2 | g11539.t1 | PANTHER | PTHR12710 | NUCLEAR PROTEIN LOCALIZATION 4 | 2 | 121 | 2.0E-16 |
| 1 | g11539.t1 | Pfam | PF05021 | NPL4 family | 2 | 120 | 1.4E-24 |
| 6 | g11539.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 61 | - |
| 7 | g11539.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 62 | 81 | - |
| 5 | g11539.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 82 | 164 | - |
| 8 | g11539.t1 | ProSitePatterns | PS01358 | Zinc finger RanBP2-type signature. | 141 | 160 | - |
| 10 | g11539.t1 | ProSiteProfiles | PS50199 | Zinc finger RanBP2 type profile. | 137 | 164 | 8.581 |
| 9 | g11539.t1 | SMART | SM00547 | zf_4 | 139 | 163 | 4.3E-5 |
| 3 | g11539.t1 | SUPERFAMILY | SSF90209 | Ran binding protein zinc finger-like | 138 | 164 | 7.26E-9 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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.
