General information for g2357.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cleavage and polyadenylation specificity factor subunit 1.
Parent gene
- The parent gene g2357 is located on chr_3: 17171615..17176095 (- 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 | g2357 | g2357.t1 | isoform | g2357.t1 | 17171615 | 17176095 |
| chr_3 | g2357 | g2357.t1 | exon | g2357.t1.exon1 | 17171615 | 17174770 |
| chr_3 | g2357 | g2357.t1 | cds | g2357.t1.CDS1 | 17171615 | 17174770 |
| chr_3 | g2357 | g2357.t1 | exon | g2357.t1.exon2 | 17174839 | 17175271 |
| chr_3 | g2357 | g2357.t1 | cds | g2357.t1.CDS2 | 17174839 | 17175271 |
| chr_3 | g2357 | g2357.t1 | exon | g2357.t1.exon3 | 17175329 | 17175869 |
| chr_3 | g2357 | g2357.t1 | cds | g2357.t1.CDS3 | 17175329 | 17175869 |
| chr_3 | g2357 | g2357.t1 | exon | g2357.t1.exon4 | 17175927 | 17176095 |
| chr_3 | g2357 | g2357.t1 | cds | g2357.t1.CDS4 | 17175927 | 17176095 |
| chr_3 | g2357 | g2357.t1 | TSS | g2357.t1 | 17176184 | 17176184 |
| chr_3 | g2357 | g2357.t1 | TTS | g2357.t1 | NA | NA |
Sequences
>g2357.t1 Gene=g2357 Length=4299
ATGTTTACAGTTTGCAAGCAAACAGTTCCAGCAACTGGAATAGAGTTTGCAATTAAATGC
AAATTCTTTAATAATCTCGAAGACAATCTTGTTATTGGCGGTGCAAATATTTTAAAAGTT
TTTCGTATAATTCCAGAAGTAGAATTGAATTCCAAGGAAAAGTTCTCAGAACATCGTCCA
CCTAACATGCGAATGGAATGTATGGCGTCATACGAACTCTTTGGGAATATAATGTCACTT
CAGTCAGTATCATTGAATAATTCACAAAGAGATGCATTATTAATCAGTTTTAAAGAAGCC
AAATTATCAGTTGTACAACATGATCCTGATCATTATGATTTAAAAACACTGTCACTACAT
TATTTTGAAGAGGAAGATGTGAAAGGAGGTTGGACAGGAAATCATAATATTCCAATTGTA
CGAGTTGATCCTGATAATCGCTGTGCTGTAATGCTCGTTTATGGTAAAAAGCTTGTTGTA
TTGCCATTCAGAAAAGACAACACCCTCGATGAAATTGAAATTCAAGATGTGAAACCTATA
AAAAAGACACCGATGCAGCTGATTGCGAAAACTCCAATTCTTCCATCGTATTTGATTACA
TTGAAGGATCTCGATGAAAAGATTGATAATGTAATTGATATTCAGTTTTTGCAAGGCTAT
TACGAGCCAACATTGCTAATTTTATACGAGCCTGTCAGAACATTTCCTGGTCGAATCGCT
GTTCGAAATGACACATGCTGTCTCGTTGCTATTTCACTTAACATTCAACAACGCGTTCAT
CCAGTTATTTGGTCTGTCACAAATCTTCCTTTTGACGCGCTTCAAGCAGTTCCTATTAAC
AAGCCAATTGGTGGCTGTCTTATCCTCTGTATTAACTCGCTAATCTATCTAAATCAAAGT
GTACCAAGTTATGGAGTTAGTCTCAACAGTACAGCTGATCATTCTACAAATTTTCCATTG
AGACCACAAGACGGCGTAAAGATTAGTCTAGATGCAGCACAAATTGCTTTCATTAGCAAT
GATAAATTGGTTCTTTCATTGAAAGATGGAGAGCTTTATGTACTCTCGTTGGTTGCTGAC
TCGATGAGAAGTGTAAGAAGCTTTCATTTTAGTCGTGCTGCATCTAGTGTCATCACAAGT
TGTGTTTGTCTTATGCACGATGAGTATCTATTTCTTGGCTCACGTTTAGGAAATTCATTA
CTACTGCGTTTCAAGGAAAAAGAAGACAATACAATAATCACAATCGACGACACAGACACG
CCAACAGTCGACAAGGATTTACAAATGTCAAAACGAATGAGATTAGAAGAGGAAGAATTG
CTGGTATATGGATCTAAAGCAACAAAGACCGCAGTGCAGTTGTCAAGTTATATCTTTGAA
GTGTGCGACAGTCTAATGAATCTTTCTCCCATTGGATATATGGCCGTTGGAGAAAGAGCA
CGTGCCGATGAGCATTTGGATGATGAAGAAGAGGATGATAAGCGTGATATAACGAAAATG
GAATTAGAAGTTGTGGCGAGCGTAGGTCATGGAAAGAATGGTGCAATTTGTGTCTTGCAC
AACACACTCAGACCGAAAATTCTCACGAGCTTCGAGCTTAATGGATGTTTGGATTTATGG
ACAGTTATTGATGATTCACAGATGAGACGTGAGACAAAGCACACATTCATGATTCTTACA
CAACGAAAAACATCAATGGTTTTAAAAACAAGTGAAGAAATTACTGATATTCATAATACA
GGATTTGCTTGCAACACACCAACAATTTTCGTTGGTAATCTCGGATCGAATCGATACATA
GTACAAGTAACATCAAAATCAATTCGATTGCTGCAAGGAACGCGTTTAGTGCAAAATATT
CCTATTGAACTCGGTTATCCACTCACAAATGTTTCAATTGCTGATCCTTATATTTGCGTT
CGTGCGTCGAATGGTCAAGTTGTCACACTTGCATTACGTGACAATCGAGAAAACACATCG
CAACGTTTGTACATGAATCGAAATCGTATAAGCGGAACTGCAGCATGCATCTCAATCTAT
CGTGATACGTCTGGCATGTTTACAACAAGTTGTGATGATTACGCTGATTTAACAAAAACT
GCCTCCGGTTCGCGTGACTTTGGTGGTTATATGAAAGCTGAGCCTGGCAAGGAAATTGAG
GACGAAGAAGATTTGCTTTATGGTGAAACTGGAAGTAAATTTAAAATGCAATCGATGATT
GACATGCAAGCGGCAACGAATGCTCAAAAGTCTGATTGGTGGCGACGTTTCTTACAATCA
GTTAAACCTTCATATTGGTTATTCGTCATTCGTGAAAATGGAAATCTTGAAATTTATTCT
GTACCTGATTTGAAGCTCATGTATATGATTACAGAAGTAGGAAATGGTAATAAAGTACTC
ACTGACGCAATGGAATTTGTTCCATTATCACAACCAGAAGATGAAAATGGCGAAACCTCA
CAAAGAATCGATCAAAGTTCTGATTTATTACCACGTGAAATATTGATGCTTGGAATGGGT
TATAACGGTACAAGACCAATTCTTTTTATTCGTATGCGAAATGATTTGTTCATCTATCGT
ACGTTCCGCTACATTCAAGGAAATTTAAAGGTTCGTTTTCGTCGCATGCGACACTCAATC
ATTTATTCATCGGTCGATCAACAAATTAAGGATGAACCAGAAAACTATGACGAGAATGAA
GATGAATTTAGTATAAATCCTGCAAATACACAAAAACTTCGTCATTTTTCAAACATAAAT
GGAATGTCTGGTGTATGCATTTGCGGTAATAGACGTTCATATTTTGTCTATCTCACAATC
AAAGGCGAACTACGAACGCATCAGTTCAATGACGATTCAATTACAATCAATAGTGGCAGC
ATGAGATGCTTTGCTGAATTTAATAATGCAAATTGTCCCAATGGTTTCCTATATTTCAAT
ATTAGTGATGATAATTTGAAAATCTCTGTATTTCCTGAACAATTTATTGTTGACGCTGAC
ACACCAATGCACAAAACCGTTTTACGTTCCACACCACAACACATTATTTATCATCCCGAT
GTAAAAGTTTATGGAGTCGTGTTGAACAGCAAAGATGTATCAAATAAATATTTCCGATTC
AATGGTGAAGACAAAGAGCTACTCGAAGATAATCGTGGCGAGCGTTTTCTTTATCCTACA
GTCGATAAATTTACATTTGTGCTTGTGTCACCATCAAATTGGCAAATTGTTCCGGAAATT
CAAATGGATTTGGAAGATTGGGAGCATGTTTGTGGACTTAAAATGGTCATGCTGGCATAC
GAAGGTGCTCAATCTGGCTTTAAAGGATATATTTGCATGGTGACAAACTTTAATTATAGT
GAAGATATTACATCACGTGGAAGAATACTGCTTTTCGATTTAATCGAGGTTGTTCCAGAG
CCTGATAAGCCATGGACAAAATATAAACTAAAGCAAATTTATGCCAAAGAACAAAAAGGT
CCAGTTTCTGCCGTAACAAGTACGATGGGATTACTCGTAGCTGCAGTTGGACAAAAAGTT
TATCTTTGGCAATTAAAGGATGGTGATTTAACTGGTGTTGCGTTTATTGATACAAATATT
TTCATTCATCAAATGGTCTCAATTAAATGTTTAATCCTTGTCGCGGATGTCTATAAATCT
GTCACAGTGTTGCGTTATCAAGAACAATTTCGAACACTTTCAATTGTCTCACGTGATTTT
AATCCATTGATGGTTTATCAAATTGAATATATTGTCGATAGAGAAATACTTGCATTTTTA
GCATCGGATGCAGAAGCGAATCTTTCAATTTTCATGTATCAACCAGAATCACGAGAGTCA
TTTGGCGGACAAAAACTCATAAGAAAAGCTGATTATCACTTGGGACAACGAGTGAATGCA
ATGTTTAGAGTCGCCTGCAACTTTAAACAGCAATATGATAAAAAAATTACTGCATACGAT
AATAAACACATGACATTTTTCTCAACACTCGATGGTGGATTTGGTTTTATTTTGCCACTT
CCTGAGAAAACATATCGACGACTTTTTATGTTGCAAAATGTGTTGCTCACCCATAGTGCT
CATCTATGTGGTCTTAATCCAAAAGCTTTTCGCACTATAAAACAATGGCGAAAAAGTCTG
ACTAATCCCGGACGAAGTGTGCTTGATGGAGAACTTATATGGCAGTATATGCATTTAAAT
CACAGTGAAAAAAATGAAATTGCGAAGAAAATTGGCACAAAAATTGACGAAATTTATCAA
GATTTATATGAAATTGACACTGTATCGAGGGTATTTTAA
>g2357.t1 Gene=g2357 Length=1432
MFTVCKQTVPATGIEFAIKCKFFNNLEDNLVIGGANILKVFRIIPEVELNSKEKFSEHRP
PNMRMECMASYELFGNIMSLQSVSLNNSQRDALLISFKEAKLSVVQHDPDHYDLKTLSLH
YFEEEDVKGGWTGNHNIPIVRVDPDNRCAVMLVYGKKLVVLPFRKDNTLDEIEIQDVKPI
KKTPMQLIAKTPILPSYLITLKDLDEKIDNVIDIQFLQGYYEPTLLILYEPVRTFPGRIA
VRNDTCCLVAISLNIQQRVHPVIWSVTNLPFDALQAVPINKPIGGCLILCINSLIYLNQS
VPSYGVSLNSTADHSTNFPLRPQDGVKISLDAAQIAFISNDKLVLSLKDGELYVLSLVAD
SMRSVRSFHFSRAASSVITSCVCLMHDEYLFLGSRLGNSLLLRFKEKEDNTIITIDDTDT
PTVDKDLQMSKRMRLEEEELLVYGSKATKTAVQLSSYIFEVCDSLMNLSPIGYMAVGERA
RADEHLDDEEEDDKRDITKMELEVVASVGHGKNGAICVLHNTLRPKILTSFELNGCLDLW
TVIDDSQMRRETKHTFMILTQRKTSMVLKTSEEITDIHNTGFACNTPTIFVGNLGSNRYI
VQVTSKSIRLLQGTRLVQNIPIELGYPLTNVSIADPYICVRASNGQVVTLALRDNRENTS
QRLYMNRNRISGTAACISIYRDTSGMFTTSCDDYADLTKTASGSRDFGGYMKAEPGKEIE
DEEDLLYGETGSKFKMQSMIDMQAATNAQKSDWWRRFLQSVKPSYWLFVIRENGNLEIYS
VPDLKLMYMITEVGNGNKVLTDAMEFVPLSQPEDENGETSQRIDQSSDLLPREILMLGMG
YNGTRPILFIRMRNDLFIYRTFRYIQGNLKVRFRRMRHSIIYSSVDQQIKDEPENYDENE
DEFSINPANTQKLRHFSNINGMSGVCICGNRRSYFVYLTIKGELRTHQFNDDSITINSGS
MRCFAEFNNANCPNGFLYFNISDDNLKISVFPEQFIVDADTPMHKTVLRSTPQHIIYHPD
VKVYGVVLNSKDVSNKYFRFNGEDKELLEDNRGERFLYPTVDKFTFVLVSPSNWQIVPEI
QMDLEDWEHVCGLKMVMLAYEGAQSGFKGYICMVTNFNYSEDITSRGRILLFDLIEVVPE
PDKPWTKYKLKQIYAKEQKGPVSAVTSTMGLLVAAVGQKVYLWQLKDGDLTGVAFIDTNI
FIHQMVSIKCLILVADVYKSVTVLRYQEQFRTLSIVSRDFNPLMVYQIEYIVDREILAFL
ASDAEANLSIFMYQPESRESFGGQKLIRKADYHLGQRVNAMFRVACNFKQQYDKKITAYD
NKHMTFFSTLDGGFGFILPLPEKTYRRLFMLQNVLLTHSAHLCGLNPKAFRTIKQWRKSL
TNPGRSVLDGELIWQYMHLNHSEKNEIAKKIGTKIDEIYQDLYEIDTVSRVF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2357.t1 | Gene3D | G3DSA:2.130.10.10 | - | 14 | 420 | 0 |
| 6 | g2357.t1 | Gene3D | G3DSA:2.130.10.10 | - | 996 | 1338 | 0 |
| 3 | g2357.t1 | PANTHER | PTHR10644:SF2 | CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 1 | 5 | 1418 | 0 |
| 4 | g2357.t1 | PANTHER | PTHR10644 | DNA REPAIR/RNA PROCESSING CPSF FAMILY | 5 | 1418 | 0 |
| 1 | g2357.t1 | Pfam | PF10433 | Mono-functional DNA-alkylating methyl methanesulfonate N-term | 91 | 679 | 0 |
| 2 | g2357.t1 | Pfam | PF03178 | CPSF A subunit region | 1064 | 1397 | 0 |
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:0005634 | nucleus | CC |
| GO:0005515 | protein binding | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14401 (cleavage and polyadenylation specificity factor subunit 1)
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.
