General information for g8769.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-processing factor 17.
Parent gene
- The parent gene g8769 is located on chr_2: 33054625..33056469 (+ 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_2 | g8769 | g8769.t1 | TSS | g8769.t1 | 33052761 | 33052761 |
| chr_2 | g8769 | g8769.t1 | isoform | g8769.t1 | 33052853 | 33054625 |
| chr_2 | g8769 | g8769.t1 | exon | g8769.t1.exon1 | 33052853 | 33054031 |
| chr_2 | g8769 | g8769.t1 | cds | g8769.t1.CDS1 | 33052853 | 33054031 |
| chr_2 | g8769 | g8769.t1 | exon | g8769.t1.exon2 | 33054092 | 33054625 |
| chr_2 | g8769 | g8769.t1 | cds | g8769.t1.CDS2 | 33054092 | 33054625 |
| chr_2 | g8769 | g8769.t1 | TTS | g8769.t1 | 33054692 | 33054692 |
Sequences
>g8769.t1 Gene=g8769 Length=1713
ATGTTAAATTTACAATCATACGGTACTAGCAGTGGCAGTAGTGATGAAGAAATAGATAAA
GAAGAAACTCCTTTGCATTTAAAGCCAATTTCAAATGAATTTTCTGTGGCGAAGTCAATT
CAAATTGTTTCAGCACCAATTGTTGTGCCTAAAGAGCGAGCATTGAATGAAAGAGCAGTG
AAACCAACAGAAAAAGAATTACAATACAATCCAAGATATGATGAGCTTTTTGCTCCAATT
CAAGGACCAGTTAATATCAATCTCACAGAACAACAGAAAATGCCAAAAAATACAGCGACT
GGATTTATTGAAGCTGCACATGTAAGTGATTTTCAATTTGAAAATCAACGAAGAACATTT
CACAGTTTTGGCTATGCACTTGATCCATCGGCGGACACAGAGATTAAATCGGATTCATAT
ATTGGACCAAATTTAGAAGGAGCTTATAATACTGATGGCAAAACTGTATTCGAGTCGACT
AAAATTAAGCCAGAAAATAAGCGAAAACGACATAAAAATGATGATCCAGCAGATTTAGAA
GGATTTGTAGGACCTTGGGGAAAATATGTAGATGAGAAATTGACAGCTGAACCATCGGAG
CAAGAAAAAGCAGAAATTGAAGAGATGATGGCAAAGAAACAGCGAAGAAATAAACGTGAA
GTTGAAGAGAAACCTGTGGAAGAGAAATCAATTCTTCACATCAACGATTCAGTTGACTAT
CAAGGAAGATCGTTCCTTCATCCTCCACATGATGTCGGTGTTAGTCTTAAAGCAGGCGCT
CATCCTGATAGATGCTTCTTGCCTAAAGCTCACATTCATTCATGGACAGGTCATACAAAG
GGCATTAGTACAATAAAACTTTTTCCAAAATCTGCTCATTTATTGCTCTCATGTGGTATG
GATGCAAAAATTAAAATTTGGGAAGTTTATAATGAACGAAGATGTGTAAGAACATATACT
GGTCATCGACAAGCTGTAAGAGATGTTGATTTCAATGCGAGAGGAACTCAATTTGTTTCT
GCTGGCTACGATAGATATTTAAAATTATGGGACACAGAAACTGGTTCTGTCGTTTCAAGA
TTTACTTCAAGAAAAATTCCTTATTGTGTGAAATTTCATCCTGATTATAATAAACAACAT
CTTTTTGTTTGTGGCACATCCGATAAGAAAATTTTATGTTGGGATACACGAAGTGGAGAA
ATTGTTCAAGAATATGATAGACATTTAGGAGCAGTTAATACAATTACATTTGTTGACGAT
AACCGAAGATTTGTGACAACATCTGATGACAAAAGCATGAGAGTTTGGGAGTGGGACATT
CCTGTCGATATGAAATATATAGCGGATCCATCAATGCACAGTATGCCTTCAGTAACACTT
TCGCCAAATGGAAAATGGCTAGCATGTCAAAGTTTGGACAATAAGATTGTAATATTTTCT
GCAATGAATCGTTTTAAAATGAATAGAAAGAAAACATTTGAAGGACATATGGTTTCTGGA
TATGCTTGCGGTCTCGATTTCTCGCCAGATATGTCATATCTTGTATCAGGTGATGGTGAT
GGAAAATGTTATATATGGGATTGGAAAACAACAAAATTATATAAAAAATGGCAAGCACAT
GATGGTGTCTGTATTAGTACTATATGGAATCCTCACGAATCAAGCAAAGTGTTTACTGCT
GGTTGGGATGGTTTAATAAAACTATGGGACTAA
>g8769.t1 Gene=g8769 Length=570
MLNLQSYGTSSGSSDEEIDKEETPLHLKPISNEFSVAKSIQIVSAPIVVPKERALNERAV
KPTEKELQYNPRYDELFAPIQGPVNINLTEQQKMPKNTATGFIEAAHVSDFQFENQRRTF
HSFGYALDPSADTEIKSDSYIGPNLEGAYNTDGKTVFESTKIKPENKRKRHKNDDPADLE
GFVGPWGKYVDEKLTAEPSEQEKAEIEEMMAKKQRRNKREVEEKPVEEKSILHINDSVDY
QGRSFLHPPHDVGVSLKAGAHPDRCFLPKAHIHSWTGHTKGISTIKLFPKSAHLLLSCGM
DAKIKIWEVYNERRCVRTYTGHRQAVRDVDFNARGTQFVSAGYDRYLKLWDTETGSVVSR
FTSRKIPYCVKFHPDYNKQHLFVCGTSDKKILCWDTRSGEIVQEYDRHLGAVNTITFVDD
NRRFVTTSDDKSMRVWEWDIPVDMKYIADPSMHSMPSVTLSPNGKWLACQSLDNKIVIFS
AMNRFKMNRKKTFEGHMVSGYACGLDFSPDMSYLVSGDGDGKCYIWDWKTTKLYKKWQAH
DGVCISTIWNPHESSKVFTAGWDGLIKLWD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g8769.t1 | CDD | cd00200 | WD40 | 271 | 570 | 8.47399E-64 |
| 10 | g8769.t1 | Coils | Coil | Coil | 199 | 224 | - |
| 9 | g8769.t1 | Gene3D | G3DSA:2.130.10.10 | - | 254 | 570 | 7.9E-92 |
| 20 | g8769.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 26 | - |
| 7 | g8769.t1 | PANTHER | PTHR43979 | PRE-MRNA-PROCESSING FACTOR 17 | 47 | 570 | 1.2E-233 |
| 1 | g8769.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 271 | 307 | 1.6E-4 |
| 3 | g8769.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 314 | 351 | 5.1E-7 |
| 5 | g8769.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 366 | 395 | 0.24 |
| 2 | g8769.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 400 | 436 | 0.039 |
| 4 | g8769.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 490 | 527 | 7.7E-6 |
| 6 | g8769.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 536 | 570 | 0.082 |
| 19 | g8769.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 295 | 309 | - |
| 21 | g8769.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 275 | 570 | 42.079 |
| 24 | g8769.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 275 | 309 | 10.408 |
| 25 | g8769.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 319 | 360 | 15.321 |
| 26 | g8769.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 405 | 437 | 12.179 |
| 22 | g8769.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 505 | 536 | 9.94 |
| 23 | g8769.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 537 | 570 | 10.642 |
| 13 | g8769.t1 | SMART | SM00320 | WD40_4 | 268 | 308 | 1.6E-5 |
| 15 | g8769.t1 | SMART | SM00320 | WD40_4 | 312 | 351 | 1.3E-9 |
| 18 | g8769.t1 | SMART | SM00320 | WD40_4 | 354 | 395 | 0.022 |
| 12 | g8769.t1 | SMART | SM00320 | WD40_4 | 398 | 437 | 4.9E-6 |
| 14 | g8769.t1 | SMART | SM00320 | WD40_4 | 443 | 480 | 14.0 |
| 17 | g8769.t1 | SMART | SM00320 | WD40_4 | 486 | 527 | 9.6E-6 |
| 16 | g8769.t1 | SMART | SM00320 | WD40_4 | 530 | 570 | 2.2E-5 |
| 8 | g8769.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 266 | 570 | 1.14E-68 |
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:0005515 | protein binding | MF |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
| GO:0071013 | catalytic step 2 spliceosome | CC |
KEGG
Orthology
- This transcript has been annotated with K12816 (pre-mRNA-processing factor 17)
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.
