General information for g11768.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-processing factor 40 homolog B.
Parent gene
- The parent gene g11768 is located on chr_1: 18342801..18343527 (+ 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 | g11768 | g11768.t8 | TSS | g11768.t8 | 18341300 | 18341300 |
| chr_1 | g11768 | g11768.t8 | isoform | g11768.t8 | 18341376 | 18342801 |
| chr_1 | g11768 | g11768.t8 | exon | g11768.t8.exon1 | 18341376 | 18342338 |
| chr_1 | g11768 | g11768.t8 | cds | g11768.t8.CDS1 | 18341774 | 18342338 |
| chr_1 | g11768 | g11768.t8 | exon | g11768.t8.exon2 | 18342398 | 18342801 |
| chr_1 | g11768 | g11768.t8 | cds | g11768.t8.CDS2 | 18342398 | 18342801 |
| chr_1 | g11768 | g11768.t8 | TTS | g11768.t8 | 18342996 | 18342996 |
Sequences
>g11768.t8 Gene=g11768 Length=1367
ATGGCCACATTCGAGTGGAGTGAGCATCGAGCACCTGATGGAAGAACTTACTATTATAAT
AATGTAACAAAAGAAAGTCGTTGGGATAAGCCAGATGTTTTAAAATCGCCGGCTGAGGTA
ATTTCATATAATTTTCAACAATAAAAAAATGAAAATGAAAATGAAAATAAATTTGTTTTT
AGCGATTATTGTCTGCATGCCCATGGAAGGAATACACATCTGATTCAGGCAAACTTTATT
ATTACAATTCAACAACAAAAGAATCGCGATGGACTGCACCTCCAGAGTTTTTAGAAGTAA
AACAAAAAATTATTTCTGAAAAGTTGATATCTTCTCCATTTACTGGCTCTGATAATATAA
GTAAAACACCTGGATCAAATGAAAACTCTTCTTCTGCAATGGATCAAGCAATGGCAGCAA
CTCTTGCACAATTAGATTCCATTGAAATGCCTGTTTTACCTAAAAAAGAGGAGCCTGCAC
CGAAAACACCAGCGGCAGCAGAAGCAACAGAAGAAGTTACAGTAGTCGAATTTAAAGATA
AAAAAGAAGCCATAGATGCATTTAAGGAGTTTTTAAAAGAGAAAAATGTTCCTGCATGCA
CATGGGAACAATGCATTAAAATAATTTCAAAGGATCCAAAATATAACACTTTCAAGAAAT
TAAACGAAAAAAAACAAGCGTTTAATGCGTACAAAACACAAAAGCAAAAGGAAGAGAAAG
AAGAACAACGTTTAAAAGCAAAACGATCTAAAGAAAATCTCGAAAAATTTTTGATGTCAC
ATGAGAAAGTAGATTCCACCACTAAATATTATCGATGTGAGGAAATGTTTTCAAATTTGG
ACGTATGGAAAGCTGTTCCTGAACAAGACAGAAGAGACTTGTTTGATGACTGTATTTTTA
ATTTATCTCAGCGTGAAAAAGAAGAAGCTAAAGTGCTTAAAAAAAGAAATATAAAAGTTT
TAAGAAAACTTTTAGAATCAATGGATTCAATCACATACCAAACTACATGGTCAGAAGCTC
AAGTATTGCTCCTAGAAAATAATGAATTTAAGAGTGATATTTCACTTCTTGGAATGGACA
AAGAAGATGCTTTGGTAGTTTTTGAGGAACATATTCGTGCACTTGAATTGGAAGAAGCTG
AAGAACGAGAAAATGAGAAGAGACGTCAAAAGAGATTACAACGAAAAAATCGTGATAACT
TTTTAGCTCTCCTTGATTTGCTTCACGAAGACGGAAAATTGACTTCAGTTTCGACTTGGG
TTGAGCTCTATCCAACAATTTCGGCTGATTTAAGATTTTCTGCTATGCTCGGACAATCAG
GTTCTACTCCACTTGATTTATTTAAGTTTTATATTGATCAATTAAAA
>g11768.t8 Gene=g11768 Length=323
MDQAMAATLAQLDSIEMPVLPKKEEPAPKTPAAAEATEEVTVVEFKDKKEAIDAFKEFLK
EKNVPACTWEQCIKIISKDPKYNTFKKLNEKKQAFNAYKTQKQKEEKEEQRLKAKRSKEN
LEKFLMSHEKVDSTTKYYRCEEMFSNLDVWKAVPEQDRRDLFDDCIFNLSQREKEEAKVL
KKRNIKVLRKLLESMDSITYQTTWSEAQVLLLENNEFKSDISLLGMDKEDALVVFEEHIR
ALELEEAEERENEKRRQKRLQRKNRDNFLALLDLLHEDGKLTSVSTWVELYPTISADLRF
SAMLGQSGSTPLDLFKFYIDQLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g11768.t8 | Coils | Coil | Coil | 88 | 124 | - |
| 15 | g11768.t8 | Coils | Coil | Coil | 244 | 264 | - |
| 13 | g11768.t8 | Gene3D | G3DSA:1.10.10.440 | - | 35 | 103 | 6.6E-20 |
| 10 | g11768.t8 | Gene3D | G3DSA:1.10.10.440 | - | 104 | 174 | 9.9E-11 |
| 11 | g11768.t8 | Gene3D | G3DSA:1.10.10.440 | - | 175 | 249 | 7.8E-9 |
| 12 | g11768.t8 | Gene3D | G3DSA:1.10.10.440 | - | 250 | 323 | 2.4E-13 |
| 19 | g11768.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 15 | 37 | - |
| 4 | g11768.t8 | PANTHER | PTHR11864 | PRE-MRNA-PROCESSING PROTEIN PRP40 | 32 | 323 | 5.0E-117 |
| 5 | g11768.t8 | PANTHER | PTHR11864:SF1 | PRE-MRNA-PROCESSING FACTOR 40 HOMOLOG B | 32 | 323 | 5.0E-117 |
| 2 | g11768.t8 | Pfam | PF01846 | FF domain | 50 | 98 | 2.9E-9 |
| 1 | g11768.t8 | Pfam | PF01846 | FF domain | 188 | 238 | 4.3E-6 |
| 3 | g11768.t8 | Pfam | PF01846 | FF domain | 263 | 318 | 3.1E-9 |
| 23 | g11768.t8 | ProSiteProfiles | PS51676 | FF domain profile. | 48 | 101 | 10.222 |
| 21 | g11768.t8 | ProSiteProfiles | PS51676 | FF domain profile. | 113 | 168 | 8.284 |
| 20 | g11768.t8 | ProSiteProfiles | PS51676 | FF domain profile. | 181 | 241 | 10.272 |
| 22 | g11768.t8 | ProSiteProfiles | PS51676 | FF domain profile. | 261 | 321 | 10.867 |
| 18 | g11768.t8 | SMART | SM00441 | FF_2 | 48 | 101 | 1.3E-8 |
| 16 | g11768.t8 | SMART | SM00441 | FF_2 | 181 | 241 | 2.5E-7 |
| 17 | g11768.t8 | SMART | SM00441 | FF_2 | 261 | 321 | 0.016 |
| 6 | g11768.t8 | SUPERFAMILY | SSF81698 | FF domain | 44 | 101 | 7.72E-13 |
| 7 | g11768.t8 | SUPERFAMILY | SSF81698 | FF domain | 106 | 175 | 2.75E-8 |
| 8 | g11768.t8 | SUPERFAMILY | SSF81698 | FF domain | 173 | 246 | 5.18E-11 |
| 9 | g11768.t8 | SUPERFAMILY | SSF81698 | FF domain | 253 | 323 | 1.16E-11 |
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:0045292 | mRNA cis splicing, via spliceosome | BP |
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.
