Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Cleavage and polyadenylation specificity factor subunit 4.

Parent gene

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.t6 TSS g11472.t6 16432803 16432803
chr_1 g11472 g11472.t6 isoform g11472.t6 16433414 16434361
chr_1 g11472 g11472.t6 exon g11472.t6.exon1 16433414 16433559
chr_1 g11472 g11472.t6 cds g11472.t6.CDS1 16433528 16433559
chr_1 g11472 g11472.t6 exon g11472.t6.exon2 16433640 16433797
chr_1 g11472 g11472.t6 cds g11472.t6.CDS2 16433640 16433797
chr_1 g11472 g11472.t6 exon g11472.t6.exon3 16433856 16434361
chr_1 g11472 g11472.t6 cds g11472.t6.CDS3 16433856 16434361
chr_1 g11472 g11472.t6 TTS g11472.t6 16434402 16434402

Sequences

>g11472.t6 Gene=g11472 Length=810
GAATTTTGTCCTTTTCGACATATTAAAGCAGAACAAAAGACAATAGTATGTAAACATTGG
CTACGAGCTCTTTGTAAAAAAGGAGATAGCTGTGAATTTTTGCATGAATATGATATGAGC
AAGATGCCTGAATGTTACTTTTTTAGTAAATATCACGCTTGTCACAAAAAGGAGTGTACA
TTTCTTCATATTGATCCTGAGAGTAAAATAAAAGATTGTGCGTGGTATGATCGAGGTTTT
TGTCGACATGGTCCTATTTGCCGTCATCGACATGTCCGTAGAGTTCTTTGTAAAAATTAC
TTAGCTGGTTTCTGTCCAGATGGTCAGTCTTGTAAATTTATGCATCCACGTTTTGAACTT
CCACCTGCATCTGATCCTAAAGATAGTCATAAGCGACCACCACAATGTCACTTTTGTAGT
GAATTGGGACACAAAATGCAAAATTGTCCAAAAATATCACAAGAACAACGTGAAATTGAG
CGTCTCAATAATATCAAAAACTCTCCTTATAGTGCACATCATAATTTACAAAAAATGCAA
AAACCAAACACAGGAGGAGTAGAAGGAAATTCAGATCAACAGCAACAACAACAACAGCAA
ATACCACCTCAACAACAGCAGCATCATAATAATCCACCTCCCACTCATCGTGGTCATTTC
AATCACCATCATAATCAAAATGGTCCGAGAGCACCATATGTGCCAAGAAAATTAGAAGAC
ATTACCTGCTTTAAATGTGGCATGAAGGGACATTACGCAAATAGATGTTATAGTTTCTTA
AATAATTCAGTAGATAATAACAGTAAATAA

>g11472.t6 Gene=g11472 Length=231
MSKMPECYFFSKYHACHKKECTFLHIDPESKIKDCAWYDRGFCRHGPICRHRHVRRVLCK
NYLAGFCPDGQSCKFMHPRFELPPASDPKDSHKRPPQCHFCSELGHKMQNCPKISQEQRE
IERLNNIKNSPYSAHHNLQKMQKPNTGGVEGNSDQQQQQQQQIPPQQQQHHNNPPPTHRG
HFNHHHNQNGPRAPYVPRKLEDITCFKCGMKGHYANRCYSFLNNSVDNNSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g11472.t6 Gene3D G3DSA:4.10.1000.10 CCCH zinc finger 1 32 7.3E-7
16 g11472.t6 Gene3D G3DSA:4.10.1000.10 CCCH zinc finger 55 131 2.7E-6
14 g11472.t6 MobiDBLite mobidb-lite consensus disorder prediction 145 174 -
3 g11472.t6 PANTHER PTHR23102:SF24 CLEAVAGE AND POLYADENYLATION-SPECIFIC FACTOR 4 1 144 1.5E-54
5 g11472.t6 PANTHER PTHR23102 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-RELATED 1 144 1.5E-54
2 g11472.t6 PANTHER PTHR23102:SF24 CLEAVAGE AND POLYADENYLATION-SPECIFIC FACTOR 4 145 220 1.5E-54
4 g11472.t6 PANTHER PTHR23102 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-RELATED 145 220 1.5E-54
1 g11472.t6 Pfam PF00642 Zinc finger C-x8-C-x5-C-x3-H type (and similar) 56 79 2.9E-7
19 g11472.t6 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 1 28 9.376
17 g11472.t6 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 29 53 8.756
18 g11472.t6 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 54 80 13.826
20 g11472.t6 ProSiteProfiles PS50158 Zinc finger CCHC-type profile. 205 218 9.653
13 g11472.t6 SMART SM00356 c3hfinal6 1 27 3.7
12 g11472.t6 SMART SM00356 c3hfinal6 29 55 0.14
11 g11472.t6 SMART SM00356 c3hfinal6 56 79 0.0074
10 g11472.t6 SMART SM00343 c2hcfinal6 97 113 0.11
9 g11472.t6 SMART SM00343 c2hcfinal6 204 220 0.023
8 g11472.t6 SUPERFAMILY SSF90229 CCCH zinc finger 55 78 4.87E-6
7 g11472.t6 SUPERFAMILY SSF57756 Retrovirus zinc finger-like domains 86 118 3.31E-6
6 g11472.t6 SUPERFAMILY SSF57756 Retrovirus zinc finger-like domains 185 222 1.5E-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 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.

Raw TPM values