Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t2 TSS g11472.t2 16432803 16432803
chr_1 g11472 g11472.t2 isoform g11472.t2 16432804 16434361
chr_1 g11472 g11472.t2 exon g11472.t2.exon1 16432804 16432892
chr_1 g11472 g11472.t2 exon g11472.t2.exon2 16432967 16433349
chr_1 g11472 g11472.t2 cds g11472.t2.CDS1 16433197 16433349
chr_1 g11472 g11472.t2 exon g11472.t2.exon3 16433414 16433559
chr_1 g11472 g11472.t2 cds g11472.t2.CDS2 16433414 16433559
chr_1 g11472 g11472.t2 exon g11472.t2.exon4 16433640 16433797
chr_1 g11472 g11472.t2 cds g11472.t2.CDS3 16433640 16433797
chr_1 g11472 g11472.t2 exon g11472.t2.exon5 16433856 16434361
chr_1 g11472 g11472.t2 cds g11472.t2.CDS4 16433856 16434361
chr_1 g11472 g11472.t2 TTS g11472.t2 16434402 16434402

Sequences

>g11472.t2 Gene=g11472 Length=1282
GATTCATTTCATCATTGCTTGGAAAATTGCATATTTTTATTTAATAAAATGAAAAGTGCA
GTGTTACTCAGCAAATTATATTTTATTGTCTAAAAAATTAAAACATCAAAAGTTTTCAAT
TTTTAATTCTAAATGTGTTTACTCATCGCTAATGATTTAAATCGATATTTTATTTAGTTT
AACGATCTTATGAAATTTTGAAAATTGATCTTGAATTTGAACTTGTAAATAAAATAAACA
ACAAATTTCCGACTCACAATTTTTATCCAAATTTATTTTGTAAAAGTTCACGATAATATT
ACAGTTAAAACATAGCAAAATGGATTACATTATAGCCAACGTTGATGGAGCTTTTTTAAA
AATAGAGACAGAGTTAAATGAACAGATTGGATGGAATGAATTGCCTTTTACAGGAATGGA
CAAATCAACTTCCGCTGTTTGTAATTTCTTTAATCAAGGAAAATGTGAAAAAGAATTTTG
TCCTTTTCGACATATTAAAGCAGAACAAAAGACAATAGTATGTAAACATTGGCTACGAGC
TCTTTGTAAAAAAGGAGATAGCTGTGAATTTTTGCATGAATATGATATGAGCAAGATGCC
TGAATGTTACTTTTTTAGTAAATATCACGCTTGTCACAAAAAGGAGTGTACATTTCTTCA
TATTGATCCTGAGAGTAAAATAAAAGATTGTGCGTGGTATGATCGAGGTTTTTGTCGACA
TGGTCCTATTTGCCGTCATCGACATGTCCGTAGAGTTCTTTGTAAAAATTACTTAGCTGG
TTTCTGTCCAGATGGTCAGTCTTGTAAATTTATGCATCCACGTTTTGAACTTCCACCTGC
ATCTGATCCTAAAGATAGTCATAAGCGACCACCACAATGTCACTTTTGTAGTGAATTGGG
ACACAAAATGCAAAATTGTCCAAAAATATCACAAGAACAACGTGAAATTGAGCGTCTCAA
TAATATCAAAAACTCTCCTTATAGTGCACATCATAATTTACAAAAAATGCAAAAACCAAA
CACAGGAGGAGTAGAAGGAAATTCAGATCAACAGCAACAACAACAACAGCAAATACCACC
TCAACAACAGCAGCATCATAATAATCCACCTCCCACTCATCGTGGTCATTTCAATCACCA
TCATAATCAAAATGGTCCGAGAGCACCATATGTGCCAAGAAAATTAGAAGACATTACCTG
CTTTAAATGTGGCATGAAGGGACATTACGCAAATAGATGTTATAGTTTCTTAAATAATTC
AGTAGATAATAACAGTAAATAA

>g11472.t2 Gene=g11472 Length=320
MDYIIANVDGAFLKIETELNEQIGWNELPFTGMDKSTSAVCNFFNQGKCEKEFCPFRHIK
AEQKTIVCKHWLRALCKKGDSCEFLHEYDMSKMPECYFFSKYHACHKKECTFLHIDPESK
IKDCAWYDRGFCRHGPICRHRHVRRVLCKNYLAGFCPDGQSCKFMHPRFELPPASDPKDS
HKRPPQCHFCSELGHKMQNCPKISQEQREIERLNNIKNSPYSAHHNLQKMQKPNTGGVEG
NSDQQQQQQQQIPPQQQQHHNNPPPTHRGHFNHHHNQNGPRAPYVPRKLEDITCFKCGMK
GHYANRCYSFLNNSVDNNSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g11472.t2 Gene3D G3DSA:4.10.1000.10 CCCH zinc finger 59 118 7.5E-24
18 g11472.t2 Gene3D G3DSA:4.10.1000.10 CCCH zinc finger 119 175 4.6E-7
16 g11472.t2 MobiDBLite mobidb-lite consensus disorder prediction 234 263 -
3 g11472.t2 PANTHER PTHR23102 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-RELATED 1 228 1.3E-89
4 g11472.t2 PANTHER PTHR23102 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-RELATED 228 309 1.3E-89
2 g11472.t2 Pfam PF00642 Zinc finger C-x8-C-x5-C-x3-H type (and similar) 63 86 9.5E-5
1 g11472.t2 Pfam PF00642 Zinc finger C-x8-C-x5-C-x3-H type (and similar) 145 168 4.4E-7
23 g11472.t2 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 35 61 11.319
19 g11472.t2 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 62 89 14.793
20 g11472.t2 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 90 117 9.376
22 g11472.t2 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 118 142 8.756
21 g11472.t2 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 143 169 13.826
24 g11472.t2 ProSiteProfiles PS50158 Zinc finger CCHC-type profile. 294 307 9.653
14 g11472.t2 SMART SM00356 c3hfinal6 36 60 0.48
13 g11472.t2 SMART SM00356 c3hfinal6 62 88 3.0E-4
11 g11472.t2 SMART SM00356 c3hfinal6 90 116 3.7
15 g11472.t2 SMART SM00356 c3hfinal6 118 144 0.14
12 g11472.t2 SMART SM00356 c3hfinal6 145 168 0.0074
9 g11472.t2 SMART SM00343 c2hcfinal6 186 202 0.11
10 g11472.t2 SMART SM00343 c2hcfinal6 293 309 0.023
8 g11472.t2 SUPERFAMILY SSF90229 CCCH zinc finger 62 87 2.35E-6
7 g11472.t2 SUPERFAMILY SSF90229 CCCH zinc finger 144 167 7.85E-6
6 g11472.t2 SUPERFAMILY SSF57756 Retrovirus zinc finger-like domains 176 207 5.93E-6
5 g11472.t2 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

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.

Raw TPM values