Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable cleavage and polyadenylation specificity factor subunit 2.

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_3 g226 g226.t1 TSS g226.t1 1872052 1872052
chr_3 g226 g226.t1 isoform g226.t1 1872123 1874441
chr_3 g226 g226.t1 exon g226.t1.exon1 1872123 1872277
chr_3 g226 g226.t1 cds g226.t1.CDS1 1872123 1872277
chr_3 g226 g226.t1 exon g226.t1.exon2 1872332 1874441
chr_3 g226 g226.t1 cds g226.t1.CDS2 1872332 1874441
chr_3 g226 g226.t1 TTS g226.t1 1874481 1874481

Sequences

>g226.t1 Gene=g226 Length=2265
ATGACTTCTATAATTAAATTACATGTAATATCTGGTGGAGCTGAAAGCGAATCACCACAA
TGTTATATTCTTCAAGTAGACGAGCTTCGACTTTTACTAGATGTCGGAATGGAAATAAAT
CAGTCATCGGTTAATTTCTTAAAAGAAATTAAGAAATATGTGCATACAGTTGATGCTGTT
CTTCTTTCATATCCCGATTTAAATCATATTGGAGCTCTTCCTTATCTCGTAGGAAAATTA
AATCTCGGATGTCAAATTTTCGCGACAATTCCTACTTTTAAAATGGGTCAAATGTTTATG
TATGATTGCTTTATGAGCCACTACAATCAATATGATTTTGATCTCTTCTCACTTGATGAT
GTTGATGCTGCTTTTGATCGAATTACTCAACTGAAATATAATCAAAGCGTTTCACTCAAA
GGAAAAGGCTATGGAGTTACAATTACTCCACTTCAAGCTGGTAGAATTATTGGTGGAACA
ATTTGGAAGATTGTTAAAGTTGGAGAAGAAGATATAATATATGCAACAGATTTCAATCAT
AAGAAAGAACGTCATTTAAATGGATGTGAACTCGAAAAATTACAAAGACCATCTCTTTTA
ATTTGTGACTCATATAATGCAAAATATCAACAAGCAAGAAGGCGTGCACGTGATGAGAAA
CTGATGACAAACATCTTACAGACACTCAGAAATAATGGTAATGTACTGATAGCCGTTGAT
ACAGCAGGGAGAGTATTAGAACTAGCACATATGCTTGATCAATTATGGAAAAATAAAGAT
TCTGGACTGATGGCTTATTCTCTTGCTTTTCTTAGCAACGTTAGTTATAATGTAATTGAA
TTTGCAAAATCACAAATTGAATGGATGAGTGATAAATTGATGAAAAGTTTCGAAGGTGCT
CGCAATAATCCATTTGCATTTAAACATCTTCGACTGATACATTCAATGAATGAGCTCTCA
AAAATTCCTGGGCCAAAAGTTGTTCTCGCTAGTTGTCCTGATCTTGAAAGTGGGTTTAGC
CGAGAGTTATTTTTACAATGGGCTCATAATTCTCACAATAGCATCATTTTAACCACACGA
ACGTCGCAAGGGACATTAGCAAGAGATTTAATTGAAAATGGTGGAAATCGAAGAATTGAA
TTAGATGTAAAACGTAGAGTTGAGCTTGAAGGAGCTGAATTGGAAGAGTATACTAGAACA
CATGAAGGTGATAAACACAGACCAACAATTTTAAAACGCGAGAAAGAAGAATCAAGTTCA
GATTCTGATTCGGATGATGATATTGAAATGAAAGTCATCACTGGAAAGCATGATATTGTA
GTGAGACCTGAAGGAAGAACCCATTCTGGATTTTTTAAATCAAGCAAAAAACAATTTGCA
ATGTTTCCAATGCATGAAGAAAGAATAAAATTTGATGAATATGGTGAAATTATTAATCTT
GATGATTACAGAATTGCAGATGCTATGATAAGTGAAGGACAAGAAGATAATAAGGAAAAT
CTTATTAAAGCTGAAGATATCAAGAAGGAAAAAGAAGAAGAAATTTTACCCATTGAAAAA
CCAACGAAATGTATTAGCAGTAGAAAAATTGTTGATATTAGAGCACAAGTTCAATTTATC
GATTTTGAAGGTCGCTCTGATGGTGAATCATTAATGAAAATTCTTTCACAATTGCGTCCA
CGTAGAGTTGTTGTGGTTAGAGGAAATGAAAGCAGCAGTCAAACTTTAGCAAATCATTGT
GAACAAAATATTGGATCGAAAGTATTTACACCACATCGAGGAGAAATAATTGATGCAACA
ACTGAATCTTCAATTTATCAAGTTCGATTAACAGAAGCACTCGTGTCAGAATTAGAATTC
CAAAAAGGAAAAGATTCAGCTGAAATAGCTTGGATAAATGGCACAATTACCATGAGAAAT
AAGCTCATTGATAACACAGCTCCAACTCCTATGATAACTGATGACGAAGATCACATCGAA
ATTACTGACGATGACAACAAAATTATCGCTCTTAATCCGATTCAACCTGACATGATGCCA
TCACATAATTTTGTGTTTCTCAATGAACTTAAACTTGCTGCATTTAAAGAAATTTTACTG
AAAAATAATATTTCCTCAGAGATTTCTGGTGGTATGTTACTTTGCTGTAATGGCACAATA
GCAGTTAAGCGAATTGATGCAGGAAAAGTCACAATTGAAGGGTGTTTGTCAGAAGAATAT
TTTAAAGTTAGAGAATTACTTTATGATCAATATGCTATTGTTTAA

>g226.t1 Gene=g226 Length=754
MTSIIKLHVISGGAESESPQCYILQVDELRLLLDVGMEINQSSVNFLKEIKKYVHTVDAV
LLSYPDLNHIGALPYLVGKLNLGCQIFATIPTFKMGQMFMYDCFMSHYNQYDFDLFSLDD
VDAAFDRITQLKYNQSVSLKGKGYGVTITPLQAGRIIGGTIWKIVKVGEEDIIYATDFNH
KKERHLNGCELEKLQRPSLLICDSYNAKYQQARRRARDEKLMTNILQTLRNNGNVLIAVD
TAGRVLELAHMLDQLWKNKDSGLMAYSLAFLSNVSYNVIEFAKSQIEWMSDKLMKSFEGA
RNNPFAFKHLRLIHSMNELSKIPGPKVVLASCPDLESGFSRELFLQWAHNSHNSIILTTR
TSQGTLARDLIENGGNRRIELDVKRRVELEGAELEEYTRTHEGDKHRPTILKREKEESSS
DSDSDDDIEMKVITGKHDIVVRPEGRTHSGFFKSSKKQFAMFPMHEERIKFDEYGEIINL
DDYRIADAMISEGQEDNKENLIKAEDIKKEKEEEILPIEKPTKCISSRKIVDIRAQVQFI
DFEGRSDGESLMKILSQLRPRRVVVVRGNESSSQTLANHCEQNIGSKVFTPHRGEIIDAT
TESSIYQVRLTEALVSELEFQKGKDSAEIAWINGTITMRNKLIDNTAPTPMITDDEDHIE
ITDDDNKIIALNPIQPDMMPSHNFVFLNELKLAAFKEILLKNNISSEISGGMLLCCNGTI
AVKRIDAGKVTIEGCLSEEYFKVRELLYDQYAIV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g226.t1 CDD cd16293 CPSF2-like_MBL-fold 11 206 2.17467E-103
8 g226.t1 Coils Coil Coil 494 514 -
7 g226.t1 Gene3D G3DSA:3.60.15.10 - 8 259 3.4E-76
11 g226.t1 MobiDBLite mobidb-lite consensus disorder prediction 398 427 -
5 g226.t1 PANTHER PTHR45922 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 2 1 754 8.9E-263
4 g226.t1 Pfam PF16661 Metallo-beta-lactamase superfamily domain 23 201 4.9E-56
2 g226.t1 Pfam PF10996 Beta-Casp domain 245 370 2.3E-20
1 g226.t1 Pfam PF07521 Zn-dependent metallo-hydrolase RNA specificity domain 531 591 4.0E-15
3 g226.t1 Pfam PF13299 Cleavage and polyadenylation factor 2 C-terminal 608 751 9.2E-26
10 g226.t1 SMART SM01027 Beta_Casp_2 245 370 3.1E-29
6 g226.t1 SUPERFAMILY SSF56281 Metallo-hydrolase/oxidoreductase 11 599 3.67E-153

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:0005847 mRNA cleavage and polyadenylation specificity factor complex CC
GO:0006379 mRNA cleavage BP
GO:0006378 mRNA polyadenylation BP

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