General information for g2654.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pre-mRNA 3’-end-processing factor FIP1.
Parent gene
- The parent gene g2654 is located on chr_3: 19361490..19362574 (+ 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 | g2654 | g2654.t1 | TSS | g2654.t1 | 19360809 | 19360809 |
| chr_3 | g2654 | g2654.t1 | isoform | g2654.t1 | 19360871 | 19362484 |
| chr_3 | g2654 | g2654.t1 | exon | g2654.t1.exon1 | 19360871 | 19361097 |
| chr_3 | g2654 | g2654.t1 | cds | g2654.t1.CDS1 | 19360871 | 19361097 |
| chr_3 | g2654 | g2654.t1 | exon | g2654.t1.exon2 | 19361161 | 19361420 |
| chr_3 | g2654 | g2654.t1 | cds | g2654.t1.CDS2 | 19361161 | 19361420 |
| chr_3 | g2654 | g2654.t1 | exon | g2654.t1.exon3 | 19361484 | 19362484 |
| chr_3 | g2654 | g2654.t1 | cds | g2654.t1.CDS3 | 19361484 | 19362484 |
| chr_3 | g2654 | g2654.t1 | TTS | g2654.t1 | 19363389 | 19363389 |
Sequences
>g2654.t1 Gene=g2654 Length=1488
ATGGCTGATAATAACGACGATGAGTGGCTTTATGGTGCAGAAGGTGAAAGAGAATCTGCA
GTAGAACAACAAGAACTTCAAAATAATGAAGTTGAGATTACATCGACAATAAAAAATGCA
AACAACATAGAGAAAACATTTGAGACATTCGATGAGCATAATTTTGAAGAAGCCGGTGAG
GAAGAGCAACTAACATCAGATGATATAAAAGATACAAATGAAGAGAGCAATAATCCAGAA
GATGAAGATAGTGACGATGATGATGATGATGACATTAATGTGGTAATTGGCGATATTAAA
TCAGGCGGTACTGCAGCTTATACAAAAGGACAAGATCAAAAGCAAAAACAGCCAGGAAGT
AAATTCAATATTGAAGAGTTTGAAAGTGTCGGTACAATTAATGGTCAGCCTGCATATGAA
TTCACAACGGAAGGTGTTGAAGATAAACCATGGAGAAAGCCTGGTGCTGATATCACAGAC
TATTTCAATTATGGTTTCAATGAAGAAACTTGGCGCGCATATTGTGAGAGACAAAAGCGA
ATGCGAATTCATGAATCTGGGATTGGTCTTGCAAGTTTAACAGCTGCACAGAATCCAGGA
GGTAACATTAATCAACAGCAAGGACCAACAAATGAAGGTAGTGGTGGAGGAAGACCATAT
ATTAATATTGGAATGAATAAAGGAATGGGAAGAGGACCAAGACCACCGAGACCTGCTGGC
ACAATTGATGTTATTGGAGCACCTTCTCAAAATCCAATTCGACCAATGGCTCCACGAGAA
AATGTTATTCAAGTTATGACAGCTGATCGACGTGAATATTCTCGTACTGTTGTGAATCAA
AATCCTCAAATGCCAATGCAGTTCAATGTACCAGCAGAGGACTTTTATAATCACGAAGAG
CAGGATGCATTCAATTATGGTTATGAACCAACTCAAGATGGAAATCAATGGGAAGGAAAT
TCAAATTGGGCGCCAAGTGAAATTAAAGAATTAACTCCGATGAATCAACCACCACCAGGA
ATGCATAATGCACCAAATATGAATATTCCACCACCTATGATGCAAATGATGCCTCCACAA
AATATGATTCCTCCTCTTATGGGGCAAATGCCAATAGTAAAACAAGAACCAGAAGATAAA
CGCGACAATCGTCGAATGGGACGAGATAACAGAGATTTTAGAGATGATAGAAGGCATGAT
GATAGAAAAAGAATGCGTGAACGTTCAAATTCAAGAGAAAGAGGCGATTTAAGAAAATCT
GATCGACCTGATCGACCCAGAGATGACCGGCCACGTTCTGATCGTGATAGATATCCTAGA
GAGAGCAGCAGTCGAAGCAGCAGACGTTCAAAATCTCGTGATCGAAGCAAAAGATCTAAA
AGTCGCGATAGGAAACGTTCTAGATCAAAGGACCACAAAAGCAGCGATGATAGAGGAAGT
CGATCTGATAAATCAAAAAGAGAACGTTCAAAAAAGGAAGATGCATAA
>g2654.t1 Gene=g2654 Length=495
MADNNDDEWLYGAEGERESAVEQQELQNNEVEITSTIKNANNIEKTFETFDEHNFEEAGE
EEQLTSDDIKDTNEESNNPEDEDSDDDDDDDINVVIGDIKSGGTAAYTKGQDQKQKQPGS
KFNIEEFESVGTINGQPAYEFTTEGVEDKPWRKPGADITDYFNYGFNEETWRAYCERQKR
MRIHESGIGLASLTAAQNPGGNINQQQGPTNEGSGGGRPYINIGMNKGMGRGPRPPRPAG
TIDVIGAPSQNPIRPMAPRENVIQVMTADRREYSRTVVNQNPQMPMQFNVPAEDFYNHEE
QDAFNYGYEPTQDGNQWEGNSNWAPSEIKELTPMNQPPPGMHNAPNMNIPPPMMQMMPPQ
NMIPPLMGQMPIVKQEPEDKRDNRRMGRDNRDFRDDRRHDDRKRMRERSNSRERGDLRKS
DRPDRPRDDRPRSDRDRYPRESSSRSSRRSKSRDRSKRSKSRDRKRSRSKDHKSSDDRGS
RSDKSKRERSKKEDA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2654.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 27 | - |
| 10 | g2654.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 48 | 91 | - |
| 9 | g2654.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 74 | 91 | - |
| 4 | g2654.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 375 | 449 | - |
| 5 | g2654.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 375 | 495 | - |
| 7 | g2654.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 450 | 468 | - |
| 8 | g2654.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 469 | 495 | - |
| 2 | g2654.t1 | PANTHER | PTHR13484 | FIP1-LIKE 1 PROTEIN | 1 | 493 | 1.5E-27 |
| 3 | g2654.t1 | PANTHER | PTHR13484:SF0 | PRE-MRNA 3’-END-PROCESSING FACTOR FIP1 | 1 | 493 | 1.5E-27 |
| 1 | g2654.t1 | Pfam | PF05182 | Fip1 motif | 143 | 182 | 2.0E-23 |
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
Orthology
- This transcript has been annotated with K14405 (pre-mRNA 3’-end-processing factor FIP1)
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.
