Gene loci information

Transcript annotation

  • This transcript has been annotated as Cleavage and polyadenylation specificity factor 73.

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 g12396 g12396.t1 TTS g12396.t1 23334381 23334381
chr_1 g12396 g12396.t1 isoform g12396.t1 23334454 23336651
chr_1 g12396 g12396.t1 exon g12396.t1.exon1 23334454 23336281
chr_1 g12396 g12396.t1 cds g12396.t1.CDS1 23334454 23336281
chr_1 g12396 g12396.t1 exon g12396.t1.exon2 23336361 23336448
chr_1 g12396 g12396.t1 cds g12396.t1.CDS2 23336361 23336448
chr_1 g12396 g12396.t1 exon g12396.t1.exon3 23336507 23336651
chr_1 g12396 g12396.t1 cds g12396.t1.CDS3 23336507 23336651
chr_1 g12396 g12396.t1 TSS g12396.t1 23336694 23336694

Sequences

>g12396.t1 Gene=g12396 Length=2061
ATGTCGACAAAAAGAAAGCCAGAAAATCAAGTTCCAGCAGAAGAGAGTGATTTACTATTG
ATACGACCGCTTGGTGCTGGTCAAGAAGTTGGACGATCATGTATTATGCTGGAATTTAAA
GGGAAAAAAATCATGCTCGATTGTGGAATTCATCCTGGCTTAGCTGGAATGGACGCTTTG
CCTTTTGTTGATCTTATTGAGCCAGATGAAATTGATTTACTTTTCATTTCACATTTCCAT
TTGGATCATTGCGGTGCTTTGCCTTGGTTCTTGCAAAAAACAAGTTTTAAAGGTCGCTGT
TTTATGACACATGCAACTAAAGCAATTTATCGATGGATGCTTTCTGATTATATCAAAGTT
AGCAATATTGCAACAGAGCAAATGCTCTACACAGAAGCTGATTTAGAAGCGAGCATGGAA
AAGATAGAAACAATCAATTTTCATGAAGAACGTGATGTTATGGGTGTAAGATTTTGGGCA
TATAATGCTGGTCATGTTTTAGGAGCTGCTATGTTCATGATTGAAATTGCTGGTGTTAAA
ATTCTCTACACAGGTGATTTTTCACGTCAAGAAGATCGTCATTTAATGGCTGCCGAAATA
CCAACAATGAAGCCTGATGTGCTCATTACTGAATCAACTTACGGCACACACATTCATGAA
AAGAGAGAAGATCGTGAAGGTCGATTTACTTCACTTGTACAAAAAATTGTTACACAAGGC
GGTCGATGCCTCATTCCAGTTTTCGCTTTAGGACGTGCTCAAGAATTGCTTCTTATTCTT
GATGAATTTTGGAGTCAAAATCCAGATTTGCAAGAAATTCCAATTTACTATGCCTCATCG
TTGGCTAAAAAATGTATGGCAGTTTATCAAACATACATTTTTGGTATGAACGACAAGATT
CGTCGTCAGATTGCAGTTAACAATCCATTTGTATTCAAACACATCTCAAATTTGAAAGGA
ATTGATCATTTCGATGATATTGGACCATCAGTTGTTATGGCATCTCCTGGTATGATGCAA
TCTGGACTATCACGTGAACTTTTTGAATCTTGGTGCAGTGATCCTAAAAATGGTGTCATT
ATTGCTGGTTATTGTGTTGAAGGTACTTTAGCTAAAACTATTCTCTCTGAACCAGAAGAA
ATTACAACAATGAATGGTCAAAAGTTGCCACTTAATATGTCAGTCGATTACATTTCTTTC
TCTGCTCACACTGACTATCAACAAACATCTGAATTTATTCGTTTGTTGAAACCACAACAT
GTTGTACTTGTTCATGGTGAACAAAATGAAATGAATCGTTTAAAATCAGCATTGCAACGT
GAATATGAAAATCAACCGAATGCAAATATAACTTTCTATAATCCAAGAAACACTCATGCT
GTTGAATTATATTTCAAGGGAGAAAAGACTGCAAAAGTTATGGGAAAGTTGGCTGTTAAA
AAAGTTGAAAATGGCGATAGTGTATCAGGAATTTTAGTAAAACGTGATTTTAAGTATCAC
ATTCTCGATGCATCTGATATCAACAAGTATACCGACATGAGCATCAGCACAGTCACACAA
AGACAATCAATGGCATTTAATGGATCGCCAGCCAGCTTGAAGCTTTTGCTTGATCGAGTA
GGTGGTGCAGGCACAGTTGAAGTGCTTGATACTGATAAGAAATTTAAAGTGTTTGATGCT
GTCGAAGTAACTTTTGATGGTAAAATTGTGATTATGGAATGGGTAGCAAATCCAGTCAAC
GATATGTTTGCATATACAATTCTTGCTAGTCTCATTCAAACAGATCTATGTGGAAGCTCA
ATTAAAAGTGCCACAACATCAACAAAAAGTGATCAAGCTCATCTCAAAGAATGCATCATT
GAAACACTTCAAGAAATGTTTGGAGAAAATGCTGTACCAAAAATGTTCAAAGGCAATTCA
TTAAAAGTGACTGTTAATAAAAAGATTGTTGAAATTGATTTGAGCACATTAGAAGTAACA
TGTGCAGAAGATGAAATTCTTAGAGATACTATATACACTGCTATCAATAAGCTCAATCAA
GTACTCGTTCAAACGAAATAA

>g12396.t1 Gene=g12396 Length=686
MSTKRKPENQVPAEESDLLLIRPLGAGQEVGRSCIMLEFKGKKIMLDCGIHPGLAGMDAL
PFVDLIEPDEIDLLFISHFHLDHCGALPWFLQKTSFKGRCFMTHATKAIYRWMLSDYIKV
SNIATEQMLYTEADLEASMEKIETINFHEERDVMGVRFWAYNAGHVLGAAMFMIEIAGVK
ILYTGDFSRQEDRHLMAAEIPTMKPDVLITESTYGTHIHEKREDREGRFTSLVQKIVTQG
GRCLIPVFALGRAQELLLILDEFWSQNPDLQEIPIYYASSLAKKCMAVYQTYIFGMNDKI
RRQIAVNNPFVFKHISNLKGIDHFDDIGPSVVMASPGMMQSGLSRELFESWCSDPKNGVI
IAGYCVEGTLAKTILSEPEEITTMNGQKLPLNMSVDYISFSAHTDYQQTSEFIRLLKPQH
VVLVHGEQNEMNRLKSALQREYENQPNANITFYNPRNTHAVELYFKGEKTAKVMGKLAVK
KVENGDSVSGILVKRDFKYHILDASDINKYTDMSISTVTQRQSMAFNGSPASLKLLLDRV
GGAGTVEVLDTDKKFKVFDAVEVTFDGKIVIMEWVANPVNDMFAYTILASLIQTDLCGSS
IKSATTSTKSDQAHLKECIIETLQEMFGENAVPKMFKGNSLKVTVNKKIVEIDLSTLEVT
CAEDEILRDTIYTAINKLNQVLVQTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g12396.t1 CDD cd16292 CPSF3-like_MBL-fold 19 212 1.03278E-148
13 g12396.t1 Coils Coil Coil 424 444 -
11 g12396.t1 Gene3D G3DSA:3.60.15.10 - 24 435 5.4E-172
12 g12396.t1 Gene3D G3DSA:3.40.50.10890 - 221 400 5.4E-172
5 g12396.t1 PANTHER PTHR11203:SF11 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 3 4 682 7.4E-295
6 g12396.t1 PANTHER PTHR11203 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR FAMILY MEMBER 4 682 7.4E-295
4 g12396.t1 Pfam PF00753 Metallo-beta-lactamase superfamily 30 198 5.2E-20
2 g12396.t1 Pfam PF10996 Beta-Casp domain 253 374 1.3E-29
1 g12396.t1 Pfam PF07521 Zn-dependent metallo-hydrolase RNA specificity domain 389 443 1.4E-15
3 g12396.t1 Pfam PF11718 Pre-mRNA 3’-end-processing endonuclease polyadenylation factor C-term 487 682 1.1E-39
10 g12396.t1 SMART SM00849 Lactamase_B_5a 31 217 7.9E-13
9 g12396.t1 SMART SM01027 Beta_Casp_2 253 374 4.6E-46
8 g12396.t1 SMART SM01098 CPSF73_100_C_2 484 685 1.4E-43
7 g12396.t1 SUPERFAMILY SSF56281 Metallo-hydrolase/oxidoreductase 16 466 6.81E-186

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

KEGG

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