General information for g10182.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pre-mRNA-splicing factor 38B.
Parent gene
- The parent gene g10182 is located on chr_1: 8139342..8139870 (+ 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 | g10182 | g10182.t20 | TSS | g10182.t20 | 8138158 | 8138158 |
| chr_1 | g10182 | g10182.t20 | isoform | g10182.t20 | 8138697 | 8139870 |
| chr_1 | g10182 | g10182.t20 | exon | g10182.t20.exon1 | 8138697 | 8138790 |
| chr_1 | g10182 | g10182.t20 | exon | g10182.t20.exon2 | 8138854 | 8138883 |
| chr_1 | g10182 | g10182.t20 | cds | g10182.t20.CDS1 | 8138876 | 8138883 |
| chr_1 | g10182 | g10182.t20 | exon | g10182.t20.exon3 | 8139024 | 8139066 |
| chr_1 | g10182 | g10182.t20 | cds | g10182.t20.CDS2 | 8139024 | 8139066 |
| chr_1 | g10182 | g10182.t20 | exon | g10182.t20.exon4 | 8139156 | 8139259 |
| chr_1 | g10182 | g10182.t20 | cds | g10182.t20.CDS3 | 8139156 | 8139259 |
| chr_1 | g10182 | g10182.t20 | exon | g10182.t20.exon5 | 8139327 | 8139870 |
| chr_1 | g10182 | g10182.t20 | cds | g10182.t20.CDS4 | 8139327 | 8139870 |
| chr_1 | g10182 | g10182.t20 | TTS | g10182.t20 | 8140068 | 8140068 |
Sequences
>g10182.t20 Gene=g10182 Length=815
TAGTGACATTATTTCAGCTGAAAACGTATCATGAAGTCATTGATGAAATCTACTATCAAG
TAAAACATCTTGAGCCTTGGGAACTTAATTCCCGAAAAACTCAAGGAAATTCAGGAATGT
GCGGGAGCGTAAGGGGAGTGGGCTCGGGTGGAATAGTTAGTAGTGCATTTTGTCTTTTAT
ACAAACTATATACACTGAAATTGACACGAAAACAGCTAAATGGTTTAATAAAGCATACAG
ATTCGCCATATATCCGTGCTTTAGGATTCATGTATATTCGCTACACTCAACCTCCTGCTG
ATTTATTTGGATGGTATGAGGAGTTTCTTCAAGATGAAGAAGAGATTGATATTAAAGCTG
GTGGAGGCCATATTTTGACAATAGGTCAAATGTGTAGACAATTCCTTGTAAAGCTCGATT
GGTTTAGTACACTCTTTCCACGAATTCCTGTTCCAATACAAAAAAGTATAGAACAGCGAT
TAAATGACTATGACAAACAAAATGGAATTGTAGCTCAACCAATTGTTTCCATCCCACAAC
AACCAGAACGACGTGAACGCTCTTCAAAAGAGTATTACAGAAGTGAAAGGAGACGTTCTC
GATCACCGATAGCGAAGCGTTCACGATCACCAACAGAAAGGCGTTATAGAGGTGACTTTG
ATGATGACGCAAGACATTCAAGACGATCACATAGCCGAGAGAAATATTCATCAAGTAAGT
CTTCAAAGTATTATAGAGATCGTTCAAGATCTCGTTCTAGAGAACGTAATGATCGAAGAA
GATACGAAGAATCGAGAAGTTCACGTCGTTATTAA
>g10182.t20 Gene=g10182 Length=232
MCGSVRGVGSGGIVSSAFCLLYKLYTLKLTRKQLNGLIKHTDSPYIRALGFMYIRYTQPP
ADLFGWYEEFLQDEEEIDIKAGGGHILTIGQMCRQFLVKLDWFSTLFPRIPVPIQKSIEQ
RLNDYDKQNGIVAQPIVSIPQQPERRERSSKEYYRSERRRSRSPIAKRSRSPTERRYRGD
FDDDARHSRRSHSREKYSSSKSSKYYRDRSRSRSRERNDRRRYEESRSSRRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10182.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 140 | 232 | - |
| 4 | g10182.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 144 | 160 | - |
| 5 | g10182.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 167 | 232 | - |
| 2 | g10182.t20 | PANTHER | PTHR23142 | UNCHARACTERIZED | 9 | 231 | 1.8E-69 |
| 3 | g10182.t20 | PANTHER | PTHR23142:SF2 | PRE-MRNA-SPLICING FACTOR 38B | 9 | 231 | 1.8E-69 |
| 1 | g10182.t20 | Pfam | PF03371 | PRP38 family | 8 | 118 | 1.4E-33 |
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.
