General information for g3854.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pre-mRNA cleavage complex 2 protein Pcf11.
Parent gene
- The parent gene g3854 is located on chr_3: 28372690..28379817 (+ 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_3 | g3854 | g3854.t3 | isoform | g3854.t3 | 28371941 | 28376830 |
| chr_3 | g3854 | g3854.t3 | exon | g3854.t3.exon1 | 28371941 | 28372126 |
| chr_3 | g3854 | g3854.t3 | exon | g3854.t3.exon2 | 28372594 | 28372854 |
| chr_3 | g3854 | g3854.t3 | cds | g3854.t3.CDS1 | 28372690 | 28372854 |
| chr_3 | g3854 | g3854.t3 | exon | g3854.t3.exon3 | 28374130 | 28374255 |
| chr_3 | g3854 | g3854.t3 | cds | g3854.t3.CDS2 | 28374130 | 28374255 |
| chr_3 | g3854 | g3854.t3 | exon | g3854.t3.exon4 | 28374324 | 28374656 |
| chr_3 | g3854 | g3854.t3 | cds | g3854.t3.CDS3 | 28374324 | 28374656 |
| chr_3 | g3854 | g3854.t3 | exon | g3854.t3.exon5 | 28374715 | 28374774 |
| chr_3 | g3854 | g3854.t3 | cds | g3854.t3.CDS4 | 28374715 | 28374774 |
| chr_3 | g3854 | g3854.t3 | exon | g3854.t3.exon6 | 28374843 | 28375524 |
| chr_3 | g3854 | g3854.t3 | cds | g3854.t3.CDS5 | 28374843 | 28375524 |
| chr_3 | g3854 | g3854.t3 | exon | g3854.t3.exon7 | 28376179 | 28376326 |
| chr_3 | g3854 | g3854.t3 | cds | g3854.t3.CDS6 | 28376179 | 28376326 |
| chr_3 | g3854 | g3854.t3 | exon | g3854.t3.exon8 | 28376394 | 28376466 |
| chr_3 | g3854 | g3854.t3 | cds | g3854.t3.CDS7 | 28376394 | 28376466 |
| chr_3 | g3854 | g3854.t3 | exon | g3854.t3.exon9 | 28376521 | 28376830 |
| chr_3 | g3854 | g3854.t3 | cds | g3854.t3.CDS8 | 28376521 | 28376829 |
| chr_3 | g3854 | g3854.t3 | TTS | g3854.t3 | 28376901 | 28376901 |
| chr_3 | g3854 | g3854.t3 | TSS | g3854.t3 | NA | NA |
Sequences
>g3854.t3 Gene=g3854 Length=2179
AATCGACATTTCGAAGTCGACAAAAGTTTTAAAACGATTTTCGAATAAAATATTTCGTCA
CAAAAAAGAAAAGAGTTTTTTTTCAAATTTTTATAATTCAAATTTTAATGGTTTTTAACA
TCACAAACAAATCAAAAATGTGCTTAATTTAATTATAAGAGTGCTATTTAAAATAATAAC
CTAAAGATTAAATTTAATCAGCCTGTATAGAATCGAGAAAACTTGTGATTGTGTATTTTA
TAAAATTGTAAAGAGTTTGTAAACATTTCAATCATCAAAAATATGGACTCTGTAAAGGAA
AAGGAAATTGAAGAGGAGTATCTTTCTTCTTTAATGGATCTTAATGTCAATAGTAAACCC
CTAATCAATATGCTAACAATGTTAGCCGAGGACAATCTCGAAAATGCAGCTATTATCGTG
CGAGCGATTGAAAAACACATCTTACAGGTGTCTCCGGAAATTAAACTCCCAATTCTCTAT
TTAATTGATTCCATCGTGAAAAATGTCGGTGATAAATACAAACAACTTTTTGCCCAAAAT
ATTGTTAACATATTTTGTGGAGTTTTTGAGAAGGTGAATGAAAAAGTTCGCGAAAAAATG
TTCAATCTACGTCAAACTTGGAATGATGTTTTTCCTCAAACGAAATTATATGCATTAGAT
GTGAAAGTTAATGTGATGGACAACAATTGGCCAATTACTGCTAAAGTTTTGCCAAAATCA
GTGCATGTGAATCCAAATTTTTTGAAGAAAACTAAAAATCCAGAGAATCAAGCGAAAGAA
GATTTGATGTTGCAGATGCAAGCAAAAGAAAGAGAACTTTTAGAATTAAAGCAAAGAAAA
ATTGAGCTGGAACTTATGGTAACGAAAAAGAAAATTGCCGAACAGGAAAAAGAGATAAAG
GGAATTGTTCCTTCTACATCAAACACAGTTAATTCGGCAATATCAATTGCACCAGTTTCT
CATCCGATGACTATGACAACATCATCAATGATGATTCCTCATCAACAAGGTAGAATTCGA
ATTGCTCCAGTAAGTTCTACTATGTTATCATCAGCACGTCCTCGTGATCCACGACTTTCA
AAATTGCGTCCACAAATTGAAGTCCCTCAACCATCTTTGCCACCAACCTCAATTTTACCT
GGTATTATGAAATTACCAAGGATACCTAAATATTCTAATGGAAATAAATCATCTTCATCT
ACAACAACATCTTCATTTAGAGATATAGATGAACGTGATTCACGCAGAAGACGCGAGAAA
GATCATGATGATTCGAGCTCGAAAGAAAAGTCGAGTAAATCGAGTTCAAGTAGAAAGTCC
AGTAAATCCGATTCACCACGAAAGAAGAGTGATGATGACAAGAAATTATCATCAAAAAAT
AGTTCTTCACATCATCATAAATCTACGTCTTCGTCATCATCACATTCACGATCTCGCTCA
TCAACAAAAAGTCCATTAAAATCAGAGGTAAAATTAAAAGTTGATGAGGTTGAATCACTT
TTTCAATCGACTGATATGGATATGAGACCTGATAGTACTACAGCAGCAGCAAGCAGTAAA
ATAAGCAAAAATCAGCTATTAGATGAACTTCTTCATGATGAAGATATGAAGTCAAATCAA
GAAATGATGATTACAACGAGTAATAACGAAGAATCCAATACAATTCAAGTAAATGGAAAA
TGTGATATAGAAGCAAAAACTGAAGAAGTTGGAAAGAAGAGATCAATTGGAGGAGAACAA
AGTGAGAGCGAGTCAACTGAACCATCAAAAAAGAAGAATAAAACCGATAATGATCCATTA
TCATTGTTTGGTAATGAAGATGTTGATTTGAGATCAGTTCCACAACAACTTGAAAAGAGA
TCAAAATCAAAGGAGAAAGCAGATTTTGAGACTGTAAGAGCGAAATTGAATGCATCAAAA
ATGAAAAGTAAAACTACAGGCGTAAAATTGTTAGAAGAAATTCAACCAGCTCCTATCAAT
GAAAATGGTCCACCATCAGAATTGGTTAGGAAAATTTTACAAAAGAAAAAGAATGATGTT
AAAGAACTAGAAGAAAAAGCTTCTTCTCCACCTATTACCACTGATCGCATTGTTAATGAC
ATAGTCATGACTGAAAAGAAAGACGAAATAGTTGATTATGGTAGTATGACAGCTGCAGAA
TTGAGAAATACTTCAGGAG
>g3854.t3 Gene=g3854 Length=632
MDSVKEKEIEEEYLSSLMDLNVNSKPLINMLTMLAEDNLENAAIIVRAIEKHILQVSPEI
KLPILYLIDSIVKNVGDKYKQLFAQNIVNIFCGVFEKVNEKVREKMFNLRQTWNDVFPQT
KLYALDVKVNVMDNNWPITAKVLPKSVHVNPNFLKKTKNPENQAKEDLMLQMQAKERELL
ELKQRKIELELMVTKKKIAEQEKEIKGIVPSTSNTVNSAISIAPVSHPMTMTTSSMMIPH
QQGRIRIAPVSSTMLSSARPRDPRLSKLRPQIEVPQPSLPPTSILPGIMKLPRIPKYSNG
NKSSSSTTTSSFRDIDERDSRRRREKDHDDSSSKEKSSKSSSSRKSSKSDSPRKKSDDDK
KLSSKNSSSHHHKSTSSSSSHSRSRSSTKSPLKSEVKLKVDEVESLFQSTDMDMRPDSTT
AAASSKISKNQLLDELLHDEDMKSNQEMMITTSNNEESNTIQVNGKCDIEAKTEEVGKKR
SIGGEQSESESTEPSKKKNKTDNDPLSLFGNEDVDLRSVPQQLEKRSKSKEKADFETVRA
KLNASKMKSKTTGVKLLEEIQPAPINENGPPSELVRKILQKKKNDVKELEEKASSPPITT
DRIVNDIVMTEKKDEIVDYGSMTAAELRNTSG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3854.t3 | CDD | cd16982 | CID_Pcf11 | 11 | 136 | 5.73965E-59 |
| 7 | g3854.t3 | Coils | Coil | Coil | 165 | 204 | - |
| 6 | g3854.t3 | Coils | Coil | Coil | 572 | 592 | - |
| 5 | g3854.t3 | Gene3D | G3DSA:1.25.40.90 | - | 2 | 130 | 3.2E-44 |
| 15 | g3854.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 253 | 432 | - |
| 11 | g3854.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 297 | 311 | - |
| 16 | g3854.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 312 | 365 | - |
| 13 | g3854.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 369 | 387 | - |
| 18 | g3854.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 388 | 408 | - |
| 19 | g3854.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 411 | 431 | - |
| 14 | g3854.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 452 | 534 | - |
| 17 | g3854.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 452 | 466 | - |
| 12 | g3854.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 468 | 503 | - |
| 10 | g3854.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 518 | 534 | - |
| 2 | g3854.t3 | PANTHER | PTHR15921:SF3 | PRE-MRNA CLEAVAGE COMPLEX 2 PROTEIN PCF11 | 8 | 534 | 1.3E-71 |
| 3 | g3854.t3 | PANTHER | PTHR15921 | PRE-MRNA CLEAVAGE COMPLEX II | 8 | 534 | 1.3E-71 |
| 1 | g3854.t3 | Pfam | PF04818 | CID domain | 20 | 121 | 3.6E-15 |
| 21 | g3854.t3 | ProSiteProfiles | PS51391 | CID domain profile. | 5 | 133 | 37.607 |
| 20 | g3854.t3 | ProSiteProfiles | PS50179 | VHS domain profile. | 28 | 117 | 12.103 |
| 9 | g3854.t3 | SMART | SM00582 | 558neu5 | 8 | 130 | 1.1E-30 |
| 4 | g3854.t3 | SUPERFAMILY | SSF48464 | ENTH/VHS domain | 7 | 139 | 1.92E-42 |
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:0006886 | intracellular protein transport | BP |
KEGG
Orthology
- This transcript has been annotated with K14400 (pre-mRNA cleavage complex 2 protein Pcf11)
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.
