General information for g3854.t1
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.t1 | TSS | g3854.t1 | 28371998 | 28371998 |
| chr_3 | g3854 | g3854.t1 | isoform | g3854.t1 | 28372690 | 28379817 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon1 | 28372690 | 28372854 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS1 | 28372690 | 28372854 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon2 | 28374130 | 28374255 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS2 | 28374130 | 28374255 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon3 | 28374324 | 28374656 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS3 | 28374324 | 28374656 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon4 | 28374715 | 28374774 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS4 | 28374715 | 28374774 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon5 | 28374843 | 28375524 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS5 | 28374843 | 28375524 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon6 | 28376167 | 28376326 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS6 | 28376167 | 28376326 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon7 | 28376394 | 28376466 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS7 | 28376394 | 28376466 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon8 | 28376521 | 28376830 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS8 | 28376521 | 28376830 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon9 | 28376886 | 28378409 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS9 | 28376886 | 28378409 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon10 | 28378473 | 28378723 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS10 | 28378473 | 28378723 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon11 | 28378783 | 28379275 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS11 | 28378783 | 28379275 |
| chr_3 | g3854 | g3854.t1 | exon | g3854.t1.exon12 | 28379342 | 28379817 |
| chr_3 | g3854 | g3854.t1 | cds | g3854.t1.CDS12 | 28379342 | 28379817 |
| chr_3 | g3854 | g3854.t1 | TTS | g3854.t1 | NA | NA |
Sequences
>g3854.t1 Gene=g3854 Length=4653
ATGGACTCTGTAAAGGAAAAGGAAATTGAAGAGGAGTATCTTTCTTCTTTAATGGATCTT
AATGTCAATAGTAAACCCCTAATCAATATGCTAACAATGTTAGCCGAGGACAATCTCGAA
AATGCAGCTATTATCGTGCGAGCGATTGAAAAACACATCTTACAGGTGTCTCCGGAAATT
AAACTCCCAATTCTCTATTTAATTGATTCCATCGTGAAAAATGTCGGTGATAAATACAAA
CAACTTTTTGCCCAAAATATTGTTAACATATTTTGTGGAGTTTTTGAGAAGGTGAATGAA
AAAGTTCGCGAAAAAATGTTCAATCTACGTCAAACTTGGAATGATGTTTTTCCTCAAACG
AAATTATATGCATTAGATGTGAAAGTTAATGTGATGGACAACAATTGGCCAATTACTGCT
AAAGTTTTGCCAAAATCAGTGCATGTGAATCCAAATTTTTTGAAGAAAACTAAAAATCCA
GAGAATCAAGCGAAAGAAGATTTGATGTTGCAGATGCAAGCAAAAGAAAGAGAACTTTTA
GAATTAAAGCAAAGAAAAATTGAGCTGGAACTTATGGTAACGAAAAAGAAAATTGCCGAA
CAGGAAAAAGAGATAAAGGGAATTGTTCCTTCTACATCAAACACAGTTAATTCGGCAATA
TCAATTGCACCAGTTTCTCATCCGATGACTATGACAACATCATCAATGATGATTCCTCAT
CAACAAGGTAGAATTCGAATTGCTCCAGTAAGTTCTACTATGTTATCATCAGCACGTCCT
CGTGATCCACGACTTTCAAAATTGCGTCCACAAATTGAAGTCCCTCAACCATCTTTGCCA
CCAACCTCAATTTTACCTGGTATTATGAAATTACCAAGGATACCTAAATATTCTAATGGA
AATAAATCATCTTCATCTACAACAACATCTTCATTTAGAGATATAGATGAACGTGATTCA
CGCAGAAGACGCGAGAAAGATCATGATGATTCGAGCTCGAAAGAAAAGTCGAGTAAATCG
AGTTCAAGTAGAAAGTCCAGTAAATCCGATTCACCACGAAAGAAGAGTGATGATGACAAG
AAATTATCATCAAAAAATAGTTCTTCACATCATCATAAATCTACGTCTTCGTCATCATCA
CATTCACGATCTCGCTCATCAACAAAAAGTCCATTAAAATCAGAGGTAAAATTAAAAGTT
GATGAGGTTGAATCACTTTTTCAATCGACTGATATGGATATGAGACCTGATAGTACTACA
GCAGCAGCAAGCAGTAAAATAAGCAAAAATCAGCTATTAGATGAACTTCTTCATGATGAA
GATATGAAGTCAAATCAAGAAATGATGATTACAACGAGTAATAACGATTTCTTTACAGAA
GAATCCAATACAATTCAAGTAAATGGAAAATGTGATATAGAAGCAAAAACTGAAGAAGTT
GGAAAGAAGAGATCAATTGGAGGAGAACAAAGTGAGAGCGAGTCAACTGAACCATCAAAA
AAGAAGAATAAAACCGATAATGATCCATTATCATTGTTTGGTAATGAAGATGTTGATTTG
AGATCAGTTCCACAACAACTTGAAAAGAGATCAAAATCAAAGGAGAAAGCAGATTTTGAG
ACTGTAAGAGCGAAATTGAATGCATCAAAAATGAAAAGTAAAACTACAGGCGTAAAATTG
TTAGAAGAAATTCAACCAGCTCCTATCAATGAAAATGGTCCACCATCAGAATTGGTTAGG
AAAATTTTACAAAAGAAAAAGAATGATGTTAAAGAACTAGAAGAAAAAGCTTCTTCTCCA
CCTATTACCACTGATCGCATTGTTAATGACATAGTCATGACTGAAAAGAAAGACGAAATA
GTTGATTATGGTAGTATGACAGCTGCAGAATTGAGAAATACTTCAGGAGTACCAGCAAGT
TTACGAAAGGAAAAAAGAAAAGAGACCAAATGGAGTCAACCAACTATGCCTTGGGGTATA
GCAGCACCTGTATTGAGTACTAGACTGATGAATAATCCAAATATTCCTCTACCGCACCAT
TTTATAAACCCATGGGAAAATAATCCGATGATTGTTGCTATGCAAAAACAAAGTCAAGTT
CCACTAGTCTTACCACAAAGTCAATCACAACCTATATTGAACAATAAAATGCGCACATTA
CGCTTAGATGGAACAAGGGATCATTTGCTTCGTTTTTATGGTGAAATTGCAATTATTTTC
AATGAATCTGGCGAAGCTCATGATATAAGATTTAGTTCAGGTCAGAGTAAAGTTGTTATT
GATGATGTATATAGTCAAGTTTTGGATTTCAATGATTCTTATAAGCCTATAATAATTGAT
GGTATTATGCATAAAATCAAATTTGGTTCACCAACTCGTGAACTTTATATTGATGAAAAT
TTTTATGAATGTTATTTCAATAATCAAATCACACAAATTGTTCTCGGCGATAAAGTTCGT
AGAGTTCGAATTGAAGGCAAAGCACCAGAAGTTAAAATTGGCAACAAACGTAAAGACGTT
GTTTTAGGATTAATCAATATGATGATTGATGCTGAAATTATGGTTCCCGTCTTTCTTGAT
ACAACCGTGCAATATTTTGAATATAAAGGACAAATTTTCACATTGCAATTTGCTGATTTC
TTCCTAAGTGTCATTATAAATAATGAGCCATTCAAAGTTGAATTTGGTGGCTTACCAAAG
AATTTTGTACTTAATGGACAAAAACATTTTATTCGTTTTACTGTTTTGCCGGATGACATT
GTTCCTGGTCAAGTTAATTTGCATGGCATGAAAAGAACACATCTCTTTAGAAATTGTAAA
TCTCCACCGCTTCCAATACAGTCTGATCCAATGATTAGAGATCGTGAAATTAATCAATTT
GTTGATAATGATGCAATTAATAAGCATTTACCAATACACCACAATCCGCCAGTAACAACA
GTTATTGAACCGCCGCCACTACAACAGCAGCAGCCACAATCAAACATCACACTACCAGAT
TTGAATATAAGTGAACTACTTCAACAATTAGTTGCTACTGGAATAATTGGAAGTAATACG
AATGCACCTTCTGCATCTACAGTTTCTAAAGAAGTAGAACAAGCACCAATAAAGCCAATT
GAACCGCAAATTAATCCATCAAAATCATCTGAACCAAAACTGAAAATTATTTCCGTCAAT
TTATCTCGACCAGAATCGATTAAAATGAGACAACAAGCTATTATTGATACTTTATATTTG
GGAATTCAATGCAGTAGTTGTGGTCTTCGATTTCCAGTTGAGCAAACAATTAAATATAGT
CAGCATTTAGACTGGCATTTTAGACAAAATCGTCGTGAACGAGATAGTAAGCGAAAAGCT
CATTCCCGTAAATGGTACTACAATAGATCAGATTGGATTAAGTATGAAGAAATTGAAGAT
CTCGACGAAAGAGAAAAGAACTTTTTTGAAACGCAACAAATGGAAGCGATGGATCAAGGA
GAAGATTCAAATGGTCTTACACGTATGACAGGACAAGAAACTTATAGTTGTCCTGCAGGA
CCTGATGATGTTAATAGATGTTGTGAAATGTGTAATGATCAATTCGATCAGTTCTTCAAT
GAAGAAACAGAAGAATGGCATTTGCGATCAGCAATTAAAGTTGATAATAAATTTTTCCAT
CCAATTTGTTATGAAGATTATAAAGCATCTTTTACGCTTGATGAATCAGGTTTAAATGAA
GCAGCAAATGATTCACAAACTGAAGCAAATGACAGTGAAGTAAAAGTTGAAGATGCAAAT
GCTGTTAAAGATGAGAAGTCTGTAATTAAAAATGAAACAGAAATTGTTAATACTAATACG
GAAGATGACGATGATGTTATTGTTTTGCCGCCTGAAGAGCCAGTAATTACTGAAATTATT
GATGAACAAGATCATGAAATGACCGAGCAAAATGAAAGTCCACAGATGCAGTCTACTATC
ATTGATGATGACATTATGATTCAGGAACCGAAAATTGAAACACAAATTGTCAATGATGAT
GATGACAGCAATGATGCTCAATGTACATCAGAAGATACAAATACTTTACCATTTATCGTT
AAAATTAAGGAAGAACCTAAGGATGATGGATATGAAGATCAAACTGAGGAAGATCCCTTC
ATTGAAGTGACATCAATCAATGAAGAATTGATGCTTGATGATGGACATACACATTCACCT
TTTCAACCGGCATTAGATGAGAATGCAGTTTTTGACGAATCATCGCTATTCTCGCAGAAT
TCTAATCATGAGTCTTCTGTAATTAATGATGACAGTTCACGACATGAACCTTCGAGTGAA
CCGCTTATGGTTGGTGGTAACAAAAATATTAAAATAGTTCTATCGTCTTTAGTCCAAAAT
AATCTATCAAATAAGGGCACAGGCTCAAATAATTTTGTAAATAATGATCAAAATGATAAT
AGCAATATAGATACAAACAATAAATTAATAGATTCCAATAGCAATGACTTACAAAGAAGA
ATCAGCGATGATCGATCAACGCGTAATGAAGATTTACAAGAAAATACTGAATTGCCTTAC
ATTGTTAAAGAGTCTCTTCAGGGTTTTAATTTTGAAAAAACTGTGACAGTGAAACGTGGA
ATCGAGAACTCTGGTTTATGCTCTATCATGTAG
>g3854.t1 Gene=g3854 Length=1550
MDSVKEKEIEEEYLSSLMDLNVNSKPLINMLTMLAEDNLENAAIIVRAIEKHILQVSPEI
KLPILYLIDSIVKNVGDKYKQLFAQNIVNIFCGVFEKVNEKVREKMFNLRQTWNDVFPQT
KLYALDVKVNVMDNNWPITAKVLPKSVHVNPNFLKKTKNPENQAKEDLMLQMQAKERELL
ELKQRKIELELMVTKKKIAEQEKEIKGIVPSTSNTVNSAISIAPVSHPMTMTTSSMMIPH
QQGRIRIAPVSSTMLSSARPRDPRLSKLRPQIEVPQPSLPPTSILPGIMKLPRIPKYSNG
NKSSSSTTTSSFRDIDERDSRRRREKDHDDSSSKEKSSKSSSSRKSSKSDSPRKKSDDDK
KLSSKNSSSHHHKSTSSSSSHSRSRSSTKSPLKSEVKLKVDEVESLFQSTDMDMRPDSTT
AAASSKISKNQLLDELLHDEDMKSNQEMMITTSNNDFFTEESNTIQVNGKCDIEAKTEEV
GKKRSIGGEQSESESTEPSKKKNKTDNDPLSLFGNEDVDLRSVPQQLEKRSKSKEKADFE
TVRAKLNASKMKSKTTGVKLLEEIQPAPINENGPPSELVRKILQKKKNDVKELEEKASSP
PITTDRIVNDIVMTEKKDEIVDYGSMTAAELRNTSGVPASLRKEKRKETKWSQPTMPWGI
AAPVLSTRLMNNPNIPLPHHFINPWENNPMIVAMQKQSQVPLVLPQSQSQPILNNKMRTL
RLDGTRDHLLRFYGEIAIIFNESGEAHDIRFSSGQSKVVIDDVYSQVLDFNDSYKPIIID
GIMHKIKFGSPTRELYIDENFYECYFNNQITQIVLGDKVRRVRIEGKAPEVKIGNKRKDV
VLGLINMMIDAEIMVPVFLDTTVQYFEYKGQIFTLQFADFFLSVIINNEPFKVEFGGLPK
NFVLNGQKHFIRFTVLPDDIVPGQVNLHGMKRTHLFRNCKSPPLPIQSDPMIRDREINQF
VDNDAINKHLPIHHNPPVTTVIEPPPLQQQQPQSNITLPDLNISELLQQLVATGIIGSNT
NAPSASTVSKEVEQAPIKPIEPQINPSKSSEPKLKIISVNLSRPESIKMRQQAIIDTLYL
GIQCSSCGLRFPVEQTIKYSQHLDWHFRQNRRERDSKRKAHSRKWYYNRSDWIKYEEIED
LDEREKNFFETQQMEAMDQGEDSNGLTRMTGQETYSCPAGPDDVNRCCEMCNDQFDQFFN
EETEEWHLRSAIKVDNKFFHPICYEDYKASFTLDESGLNEAANDSQTEANDSEVKVEDAN
AVKDEKSVIKNETEIVNTNTEDDDDVIVLPPEEPVITEIIDEQDHEMTEQNESPQMQSTI
IDDDIMIQEPKIETQIVNDDDDSNDAQCTSEDTNTLPFIVKIKEEPKDDGYEDQTEEDPF
IEVTSINEELMLDDGHTHSPFQPALDENAVFDESSLFSQNSNHESSVINDDSSRHEPSSE
PLMVGGNKNIKIVLSSLVQNNLSNKGTGSNNFVNNDQNDNSNIDTNNKLIDSNSNDLQRR
ISDDRSTRNEDLQENTELPYIVKESLQGFNFEKTVTVKRGIENSGLCSIM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3854.t1 | CDD | cd16982 | CID_Pcf11 | 11 | 136 | 1.94941E-57 |
| 9 | g3854.t1 | Coils | Coil | Coil | 165 | 204 | - |
| 8 | g3854.t1 | Coils | Coil | Coil | 576 | 596 | - |
| 7 | g3854.t1 | Gene3D | G3DSA:1.25.40.90 | - | 2 | 130 | 1.2E-43 |
| 14 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 253 | 430 | - |
| 12 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 297 | 311 | - |
| 19 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 312 | 365 | - |
| 15 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 369 | 387 | - |
| 22 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 388 | 408 | - |
| 17 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 411 | 430 | - |
| 16 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 467 | 538 | - |
| 21 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 472 | 507 | - |
| 20 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 522 | 538 | - |
| 13 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1418 | 1441 | - |
| 18 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1486 | 1512 | - |
| 23 | g3854.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1497 | 1512 | - |
| 2 | g3854.t1 | PANTHER | PTHR15921:SF3 | PRE-MRNA CLEAVAGE COMPLEX 2 PROTEIN PCF11 | 8 | 539 | 3.2E-148 |
| 4 | g3854.t1 | PANTHER | PTHR15921 | PRE-MRNA CLEAVAGE COMPLEX II | 8 | 539 | 3.2E-148 |
| 3 | g3854.t1 | PANTHER | PTHR15921:SF3 | PRE-MRNA CLEAVAGE COMPLEX 2 PROTEIN PCF11 | 487 | 1263 | 3.2E-148 |
| 5 | g3854.t1 | PANTHER | PTHR15921 | PRE-MRNA CLEAVAGE COMPLEX II | 487 | 1263 | 3.2E-148 |
| 1 | g3854.t1 | Pfam | PF04818 | CID domain | 20 | 121 | 1.2E-14 |
| 25 | g3854.t1 | ProSiteProfiles | PS51391 | CID domain profile. | 5 | 133 | 37.607 |
| 24 | g3854.t1 | ProSiteProfiles | PS50179 | VHS domain profile. | 28 | 117 | 12.103 |
| 11 | g3854.t1 | SMART | SM00582 | 558neu5 | 8 | 130 | 1.1E-30 |
| 6 | g3854.t1 | SUPERFAMILY | SSF48464 | ENTH/VHS domain | 8 | 139 | 7.2E-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.
