General information for g10182.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t2 | TSS | g10182.t2 | 8137442 | 8137442 |
| chr_1 | g10182 | g10182.t2 | isoform | g10182.t2 | 8138263 | 8139870 |
| chr_1 | g10182 | g10182.t2 | exon | g10182.t2.exon1 | 8138263 | 8138278 |
| chr_1 | g10182 | g10182.t2 | cds | g10182.t2.CDS1 | 8138263 | 8138278 |
| chr_1 | g10182 | g10182.t2 | exon | g10182.t2.exon2 | 8138363 | 8138476 |
| chr_1 | g10182 | g10182.t2 | cds | g10182.t2.CDS2 | 8138363 | 8138476 |
| chr_1 | g10182 | g10182.t2 | exon | g10182.t2.exon3 | 8138563 | 8138568 |
| chr_1 | g10182 | g10182.t2 | cds | g10182.t2.CDS3 | 8138563 | 8138568 |
| chr_1 | g10182 | g10182.t2 | exon | g10182.t2.exon4 | 8138700 | 8138790 |
| chr_1 | g10182 | g10182.t2 | cds | g10182.t2.CDS4 | 8138700 | 8138790 |
| chr_1 | g10182 | g10182.t2 | exon | g10182.t2.exon5 | 8138854 | 8138883 |
| chr_1 | g10182 | g10182.t2 | cds | g10182.t2.CDS5 | 8138854 | 8138883 |
| chr_1 | g10182 | g10182.t2 | exon | g10182.t2.exon6 | 8139024 | 8139066 |
| chr_1 | g10182 | g10182.t2 | cds | g10182.t2.CDS6 | 8139024 | 8139066 |
| chr_1 | g10182 | g10182.t2 | exon | g10182.t2.exon7 | 8139156 | 8139259 |
| chr_1 | g10182 | g10182.t2 | cds | g10182.t2.CDS7 | 8139156 | 8139259 |
| chr_1 | g10182 | g10182.t2 | exon | g10182.t2.exon8 | 8139327 | 8139870 |
| chr_1 | g10182 | g10182.t2 | cds | g10182.t2.CDS8 | 8139327 | 8139870 |
| chr_1 | g10182 | g10182.t2 | TTS | g10182.t2 | 8140068 | 8140068 |
Sequences
>g10182.t2 Gene=g10182 Length=948
ATGGCGGATGAACAAGAATATAGTGGAGGAAAAAAGAAAAATAATAGTTTACCTATCTAT
GGAAATCATGAAACGATGAATCTTAATAACTTAATTTTAACAAATATTCAATCAAGTGTT
TATTTCAAAGGTATGTTGACATTATTTCAGCTGAAAACGTATCATGAAGTCATTGATGAA
ATCTACTATCAAGTAAAACATCTTGAGCCTTGGGAACTTAATTCCCGAAAAACTCAAGGA
AATTCAGGAATGTGCGGGAGCGTAAGGGGAGTGGGCTCGGGTGGAATAGTTAGTAGTGCA
TTTTGTCTTTTATACAAACTATATACACTGAAATTGACACGAAAACAGCTAAATGGTTTA
ATAAAGCATACAGATTCGCCATATATCCGTGCTTTAGGATTCATGTATATTCGCTACACT
CAACCTCCTGCTGATTTATTTGGATGGTATGAGGAGTTTCTTCAAGATGAAGAAGAGATT
GATATTAAAGCTGGTGGAGGCCATATTTTGACAATAGGTCAAATGTGTAGACAATTCCTT
GTAAAGCTCGATTGGTTTAGTACACTCTTTCCACGAATTCCTGTTCCAATACAAAAAAGT
ATAGAACAGCGATTAAATGACTATGACAAACAAAATGGAATTGTAGCTCAACCAATTGTT
TCCATCCCACAACAACCAGAACGACGTGAACGCTCTTCAAAAGAGTATTACAGAAGTGAA
AGGAGACGTTCTCGATCACCGATAGCGAAGCGTTCACGATCACCAACAGAAAGGCGTTAT
AGAGGTGACTTTGATGATGACGCAAGACATTCAAGACGATCACATAGCCGAGAGAAATAT
TCATCAAGTAAGTCTTCAAAGTATTATAGAGATCGTTCAAGATCTCGTTCTAGAGAACGT
AATGATCGAAGAAGATACGAAGAATCGAGAAGTTCACGTCGTTATTAA
>g10182.t2 Gene=g10182 Length=315
MADEQEYSGGKKKNNSLPIYGNHETMNLNNLILTNIQSSVYFKGMLTLFQLKTYHEVIDE
IYYQVKHLEPWELNSRKTQGNSGMCGSVRGVGSGGIVSSAFCLLYKLYTLKLTRKQLNGL
IKHTDSPYIRALGFMYIRYTQPPADLFGWYEEFLQDEEEIDIKAGGGHILTIGQMCRQFL
VKLDWFSTLFPRIPVPIQKSIEQRLNDYDKQNGIVAQPIVSIPQQPERRERSSKEYYRSE
RRRSRSPIAKRSRSPTERRYRGDFDDDARHSRRSHSREKYSSSKSSKYYRDRSRSRSRER
NDRRRYEESRSSRRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g10182.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 223 | 315 | - |
| 6 | g10182.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 227 | 243 | - |
| 5 | g10182.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 250 | 315 | - |
| 2 | g10182.t2 | PANTHER | PTHR23142 | UNCHARACTERIZED | 7 | 314 | 6.4E-101 |
| 3 | g10182.t2 | PANTHER | PTHR23142:SF2 | PRE-MRNA-SPLICING FACTOR 38B | 7 | 314 | 6.4E-101 |
| 1 | g10182.t2 | Pfam | PF03371 | PRP38 family | 18 | 201 | 2.2E-49 |
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 transcript has been annotated with K12850 (pre-mRNA-splicing factor 38B)
Pathway
- This transcript belongs to the following pathways
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.
