General information for g11472.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cleavage and polyadenylation specificity factor subunit 4.
Parent gene
- The parent gene g11472 is located on chr_1: 16433414..16434361 (+ 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 | g11472 | g11472.t3 | TSS | g11472.t3 | 16432803 | 16432803 |
| chr_1 | g11472 | g11472.t3 | isoform | g11472.t3 | 16432804 | 16434361 |
| chr_1 | g11472 | g11472.t3 | exon | g11472.t3.exon1 | 16432804 | 16432935 |
| chr_1 | g11472 | g11472.t3 | exon | g11472.t3.exon2 | 16433182 | 16433349 |
| chr_1 | g11472 | g11472.t3 | cds | g11472.t3.CDS1 | 16433197 | 16433349 |
| chr_1 | g11472 | g11472.t3 | exon | g11472.t3.exon3 | 16433414 | 16433559 |
| chr_1 | g11472 | g11472.t3 | cds | g11472.t3.CDS2 | 16433414 | 16433559 |
| chr_1 | g11472 | g11472.t3 | exon | g11472.t3.exon4 | 16433640 | 16433797 |
| chr_1 | g11472 | g11472.t3 | cds | g11472.t3.CDS3 | 16433640 | 16433797 |
| chr_1 | g11472 | g11472.t3 | exon | g11472.t3.exon5 | 16433856 | 16434361 |
| chr_1 | g11472 | g11472.t3 | cds | g11472.t3.CDS4 | 16433856 | 16434361 |
| chr_1 | g11472 | g11472.t3 | TTS | g11472.t3 | 16434402 | 16434402 |
Sequences
>g11472.t3 Gene=g11472 Length=1110
GATTCATTTCATCATTGCTTGGAAAATTGCATATTTTTATTTAATAAAATGAAAAGTGCA
GTGTTACTCAGCAAATTATATTTTATTGTGTAAATACTTATTTTAAATATATAAATCTAC
TGCTTTTTTGAGTTAAAACATAGCAAAATGGATTACATTATAGCCAACGTTGATGGAGCT
TTTTTAAAAATAGAGACAGAGTTAAATGAACAGATTGGATGGAATGAATTGCCTTTTACA
GGAATGGACAAATCAACTTCCGCTGTTTGTAATTTCTTTAATCAAGGAAAATGTGAAAAA
GAATTTTGTCCTTTTCGACATATTAAAGCAGAACAAAAGACAATAGTATGTAAACATTGG
CTACGAGCTCTTTGTAAAAAAGGAGATAGCTGTGAATTTTTGCATGAATATGATATGAGC
AAGATGCCTGAATGTTACTTTTTTAGTAAATATCACGCTTGTCACAAAAAGGAGTGTACA
TTTCTTCATATTGATCCTGAGAGTAAAATAAAAGATTGTGCGTGGTATGATCGAGGTTTT
TGTCGACATGGTCCTATTTGCCGTCATCGACATGTCCGTAGAGTTCTTTGTAAAAATTAC
TTAGCTGGTTTCTGTCCAGATGGTCAGTCTTGTAAATTTATGCATCCACGTTTTGAACTT
CCACCTGCATCTGATCCTAAAGATAGTCATAAGCGACCACCACAATGTCACTTTTGTAGT
GAATTGGGACACAAAATGCAAAATTGTCCAAAAATATCACAAGAACAACGTGAAATTGAG
CGTCTCAATAATATCAAAAACTCTCCTTATAGTGCACATCATAATTTACAAAAAATGCAA
AAACCAAACACAGGAGGAGTAGAAGGAAATTCAGATCAACAGCAACAACAACAACAGCAA
ATACCACCTCAACAACAGCAGCATCATAATAATCCACCTCCCACTCATCGTGGTCATTTC
AATCACCATCATAATCAAAATGGTCCGAGAGCACCATATGTGCCAAGAAAATTAGAAGAC
ATTACCTGCTTTAAATGTGGCATGAAGGGACATTACGCAAATAGATGTTATAGTTTCTTA
AATAATTCAGTAGATAATAACAGTAAATAA
>g11472.t3 Gene=g11472 Length=320
MDYIIANVDGAFLKIETELNEQIGWNELPFTGMDKSTSAVCNFFNQGKCEKEFCPFRHIK
AEQKTIVCKHWLRALCKKGDSCEFLHEYDMSKMPECYFFSKYHACHKKECTFLHIDPESK
IKDCAWYDRGFCRHGPICRHRHVRRVLCKNYLAGFCPDGQSCKFMHPRFELPPASDPKDS
HKRPPQCHFCSELGHKMQNCPKISQEQREIERLNNIKNSPYSAHHNLQKMQKPNTGGVEG
NSDQQQQQQQQIPPQQQQHHNNPPPTHRGHFNHHHNQNGPRAPYVPRKLEDITCFKCGMK
GHYANRCYSFLNNSVDNNSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g11472.t3 | Gene3D | G3DSA:4.10.1000.10 | CCCH zinc finger | 59 | 118 | 7.5E-24 |
| 18 | g11472.t3 | Gene3D | G3DSA:4.10.1000.10 | CCCH zinc finger | 119 | 175 | 4.6E-7 |
| 16 | g11472.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 234 | 263 | - |
| 3 | g11472.t3 | PANTHER | PTHR23102 | CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-RELATED | 1 | 228 | 1.3E-89 |
| 4 | g11472.t3 | PANTHER | PTHR23102 | CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-RELATED | 228 | 309 | 1.3E-89 |
| 2 | g11472.t3 | Pfam | PF00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar) | 63 | 86 | 9.5E-5 |
| 1 | g11472.t3 | Pfam | PF00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar) | 145 | 168 | 4.4E-7 |
| 23 | g11472.t3 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 35 | 61 | 11.319 |
| 19 | g11472.t3 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 62 | 89 | 14.793 |
| 20 | g11472.t3 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 90 | 117 | 9.376 |
| 22 | g11472.t3 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 118 | 142 | 8.756 |
| 21 | g11472.t3 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 143 | 169 | 13.826 |
| 24 | g11472.t3 | ProSiteProfiles | PS50158 | Zinc finger CCHC-type profile. | 294 | 307 | 9.653 |
| 14 | g11472.t3 | SMART | SM00356 | c3hfinal6 | 36 | 60 | 0.48 |
| 13 | g11472.t3 | SMART | SM00356 | c3hfinal6 | 62 | 88 | 3.0E-4 |
| 11 | g11472.t3 | SMART | SM00356 | c3hfinal6 | 90 | 116 | 3.7 |
| 15 | g11472.t3 | SMART | SM00356 | c3hfinal6 | 118 | 144 | 0.14 |
| 12 | g11472.t3 | SMART | SM00356 | c3hfinal6 | 145 | 168 | 0.0074 |
| 9 | g11472.t3 | SMART | SM00343 | c2hcfinal6 | 186 | 202 | 0.11 |
| 10 | g11472.t3 | SMART | SM00343 | c2hcfinal6 | 293 | 309 | 0.023 |
| 8 | g11472.t3 | SUPERFAMILY | SSF90229 | CCCH zinc finger | 62 | 87 | 2.35E-6 |
| 7 | g11472.t3 | SUPERFAMILY | SSF90229 | CCCH zinc finger | 144 | 167 | 7.85E-6 |
| 6 | g11472.t3 | SUPERFAMILY | SSF57756 | Retrovirus zinc finger-like domains | 176 | 207 | 5.93E-6 |
| 5 | g11472.t3 | SUPERFAMILY | SSF57756 | Retrovirus zinc finger-like domains | 274 | 311 | 1.92E-5 |
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:0046872 | metal ion binding | MF |
| GO:0008270 | zinc ion binding | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14404 (cleavage and polyadenylation specificity factor subunit 4)
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.
