General information for g11061.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U1 small nuclear ribonucleoprotein 70 kDa.
Parent gene
- The parent gene g11061 is located on chr_1: 13739132..13741509 (+ 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 | g11061 | g11061.t8 | TSS | g11061.t8 | 13736261 | 13736261 |
| chr_1 | g11061 | g11061.t8 | isoform | g11061.t8 | 13736911 | 13739132 |
| chr_1 | g11061 | g11061.t8 | exon | g11061.t8.exon1 | 13736911 | 13737044 |
| chr_1 | g11061 | g11061.t8 | cds | g11061.t8.CDS1 | 13736969 | 13737044 |
| chr_1 | g11061 | g11061.t8 | exon | g11061.t8.exon2 | 13738147 | 13738386 |
| chr_1 | g11061 | g11061.t8 | cds | g11061.t8.CDS2 | 13738147 | 13738386 |
| chr_1 | g11061 | g11061.t8 | exon | g11061.t8.exon3 | 13738446 | 13738611 |
| chr_1 | g11061 | g11061.t8 | cds | g11061.t8.CDS3 | 13738446 | 13738611 |
| chr_1 | g11061 | g11061.t8 | exon | g11061.t8.exon4 | 13738673 | 13738797 |
| chr_1 | g11061 | g11061.t8 | cds | g11061.t8.CDS4 | 13738673 | 13738797 |
| chr_1 | g11061 | g11061.t8 | exon | g11061.t8.exon5 | 13739002 | 13739132 |
| chr_1 | g11061 | g11061.t8 | cds | g11061.t8.CDS5 | 13739002 | 13739132 |
| chr_1 | g11061 | g11061.t8 | TTS | g11061.t8 | 13739293 | 13739293 |
Sequences
>g11061.t8 Gene=g11061 Length=796
ATCAGAATCGAAATTAAGAAGAGAATTTGAAGTGTATGGACCAATAAGGAAAATTATAAT
GATCCACGATCAAGATTCAGGCAAACCTCGTGGTTATGCGTTTATTGAGTACGAACATGA
AAGAGACATGCATTCTGCATACAAACATGCTGATGGTAAAAAAATTGATGGTAGAAGGGT
ATTGGTTGACGTTGAACGTGCAAGAACAGTTAAAGGATGGTTACCTCGAAGACTTGGAGG
TGGTTTAGGTGGAACAAGACGTGGTGGTGCTGAGGTAAATATTAAGCACAGTGGACGAGA
AGATAATGTACGTGAAAAGGAGAGATATCGTCTTGAAAGAGAAAGAGAAGATAATCGTCG
TCTTGATGATAGAAGATTTGATAGAAGACGATCTCGATCACATGAAAAAAGTCGTGAAAG
AAGACGATCTCGATCGAAAGAACGTAGAAGACATAGGTCGCGTGAAGAAGATTATGAAAG
ACATGATAGAAGAGAAAAATCGCGTGAGAAGAAACGCCGAAGAACACGTTCTAGAGATCG
AGATCGTTCTGAACGTAAACGCGATAAACGTGATCGTTCTAGATCACGTGAAAGACGCCG
TGATAAGGACAAGAAAGAGCGTAAACCAGAGTTCGATATTAAAATTAAGGAAGAACCCAT
TGATGATTATCCGGACTACACGCAACATGATTATGGTCAATATGCCAATCAAGTTAAGTA
TGAATCAGGTGATGAAGAAAAATATAGACCAAATGAGCAAGATGGAGCCGCTTATGGTTA
TCGACAAGATTATTAA
>g11061.t8 Gene=g11061 Length=245
MIHDQDSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERARTVKGWLPRRLG
GGLGGTRRGGAEVNIKHSGREDNVREKERYRLEREREDNRRLDDRRFDRRRSRSHEKSRE
RRRSRSKERRRHRSREEDYERHDRREKSREKKRRRTRSRDRDRSERKRDKRDRSRSRERR
RDKDKKERKPEFDIKIKEEPIDDYPDYTQHDYGQYANQVKYESGDEEKYRPNEQDGAAYG
YRQDY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g11061.t8 | Coils | Coil | Coil | 85 | 105 | - |
| 12 | g11061.t8 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 82 | 5.2E-22 |
| 7 | g11061.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 62 | 86 | - |
| 11 | g11061.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 108 | 207 | - |
| 9 | g11061.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 115 | 130 | - |
| 6 | g11061.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 131 | 146 | - |
| 5 | g11061.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 147 | 161 | - |
| 8 | g11061.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 162 | 206 | - |
| 10 | g11061.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 221 | 245 | - |
| 2 | g11061.t8 | PANTHER | PTHR13952 | U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KD | 1 | 182 | 5.2E-42 |
| 3 | g11061.t8 | PANTHER | PTHR13952:SF5 | U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KDA | 1 | 182 | 5.2E-42 |
| 1 | g11061.t8 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 2 | 41 | 6.2E-8 |
| 14 | g11061.t8 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 1 | 48 | 10.889 |
| 4 | g11061.t8 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 1 | 70 | 3.53E-15 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003676 | nucleic acid binding | MF |
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.
