General information for g9509.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative CLK4-associating serine/arginine rich protein.
Parent gene
- The parent gene g9509 is located on chr_1: 3826386..3827339 (- 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_1 | g9509 | g9509.t1 | TTS | g9509.t1 | 3824129 | 3824129 |
| chr_1 | g9509 | g9509.t1 | isoform | g9509.t1 | 3824306 | 3827339 |
| chr_1 | g9509 | g9509.t1 | exon | g9509.t1.exon1 | 3824306 | 3824718 |
| chr_1 | g9509 | g9509.t1 | cds | g9509.t1.CDS1 | 3824306 | 3824718 |
| chr_1 | g9509 | g9509.t1 | exon | g9509.t1.exon2 | 3824809 | 3824899 |
| chr_1 | g9509 | g9509.t1 | cds | g9509.t1.CDS2 | 3824809 | 3824899 |
| chr_1 | g9509 | g9509.t1 | exon | g9509.t1.exon3 | 3825156 | 3825201 |
| chr_1 | g9509 | g9509.t1 | cds | g9509.t1.CDS3 | 3825156 | 3825201 |
| chr_1 | g9509 | g9509.t1 | exon | g9509.t1.exon4 | 3825270 | 3826994 |
| chr_1 | g9509 | g9509.t1 | cds | g9509.t1.CDS4 | 3825270 | 3826994 |
| chr_1 | g9509 | g9509.t1 | exon | g9509.t1.exon5 | 3827083 | 3827165 |
| chr_1 | g9509 | g9509.t1 | cds | g9509.t1.CDS5 | 3827083 | 3827165 |
| chr_1 | g9509 | g9509.t1 | exon | g9509.t1.exon6 | 3827241 | 3827339 |
| chr_1 | g9509 | g9509.t1 | cds | g9509.t1.CDS6 | 3827241 | 3827339 |
| chr_1 | g9509 | g9509.t1 | TSS | g9509.t1 | 3827483 | 3827483 |
Sequences
>g9509.t1 Gene=g9509 Length=2457
ATGTGGCACGAAGCAAGAAAACAAGAAAAGAAAATTAAAGGAATGCTCGTAGACTATAGA
AAACGAGCTGATAGAAGAAAAGAATATTACGACAAGATAAAAGCAGACCCAATTAGATTT
ATGCAAGTACATGGACGGAAATGTAAAATTCATTTTGAAGCCGTGGATTCATCGGATCAT
ATGATGAATTTTAGAATTGAAGGCGAAGACATTTTGATTGATCGCTTTGATGTAAGATCA
CATTTGGATTACATTTCTACACCAAAAAAGCAAGAAGAGTCAACAGAGTCGGAAAAAATT
TCTGAAGAAGAAAGGCAGTTGAACTATGAACGATATAAAATTTTAGCATCAAATGAATTT
TTGGGAATAACCGAGGAGAATTTTCTTAAACAAATACAAATAGAGGAACAATTTGGTAGT
GCTGATAAAAGTGATGATAAAAGCAAAAAGAAAAATAGTCAAGCAACAGCTGCAATTGGA
TATACTTATGAGGACTCTACAGCTACAGCAAATATCGTACCATTCTCACAACAAATACTT
TCAATTGAAGCCTCATCATCATCATCTCGTTATGAAGAATTTGCAAAAGATTATTCAGAT
GATTCTGATATTGACATGGATGTGACAATTGATGTCAAAAAAATTGGTACACAACAAGCA
CATGAGTTAAATAATTATGGGAAAAAATACGGCATGCATTCAAATGATTTATTCTCGTTT
CTCACGCGTGACGAAGATGAGAAAATGTCGTTAAAGGCAATGAAAGAACAAGAAGCTGAT
AAAATGTTGAGTGGCGGTAGAAAAAGTCGACGTGAAAGACGCTCGCAAAGGGAAAAGAGA
ATTCTTGGAAGACCACTTAATTCACCACCTTCGTATGCAGCTAAAGAGGAAGAAAAAGAA
AAACCACTTGAAGATGATGATGAAGATGAAAGTGATAAAAGTTCACGATCAAAATCACCA
TCGGTTGAGAAAATAACATTTATCACATCATTTGGAGGAGAAGAAGAGTTGCAACCGCAT
CCAAAAATTTCGATACCTCTCAAGAAAACTGCATCACAGAAACTCATTAGTAATTTGAGG
AAAAATGAAACATTTTCTGATATGGTTAAACGAAATGCAGAAAAATTGTCGCATATGAAT
GAATATGAAAAATCAAAAAATTCGAGACGTAGTCGAAGTAGAAGTTCAGATCATAGAAGA
AAACGTTCCAGAAGTAGATCATCACGAAGACGTTACAGTTCTCGTTCAAGATCTCGATCA
AGAAGAAGGCATGATTATAGTTCAAGAAGTAGAAGTAGAGATAGGCGCAGTTACCGTAAT
CGCTCTTCAAAATCATATAGTGTATCATCTTATTCCAGTCGTGATCGTCGTAGTTCAAGA
AGTACTTCAAGAAGACGTTATAGAAGTCGTCACCGTTCGCGTAATTATAGAAGAACTTCC
TATCGAAAATCTTATAGTCGCCATCGTTCAACAAGTCCAGAAGAGAAAACTTATAAAAAA
TCAACTTCAAGAAGACGTTCTGATTCACGTTCACGTAGAAAATCATCAAATCGTAGGCAT
TCTACTAGTCGATCTTTTTCTTCTTCGTCTTCATCAACAACTTCAAGTTCTTCGAGTAGC
TCTAGCTCAAGTAGTTCCAGTTCAAAAAGTTCACCAGTACACCGAAAATCAGTTGAAACA
AAATCAACAAAGTCATCGCCATTATCATCTTTACCACGAAGTAAATCAAAATCAAAATCA
CCATTAAAGTTAAAAAGATCAAGCAGTAGAGAAGCTGAATTAGTTAAAAAAGAATCACCA
GCGCCAATTAAAAGATATTATGGTAGAAAACGAGATGATGATAGTTCAAGTTCACTTAGC
ATTGATAGTGATGATGATGATGATAAAAAGATTGGCTCAAATGAGAGTTCCACAAATGAT
GCATACAAAGTCAATAGGTCTGCAGAGCTCAAAATCAATATGAGTAAATCAACAGTTGGA
CCATCTGTTAGTAATCCAAGAGAAAAGTTGAAGAAAAAGATGCAAATTTTACTAAACAAG
CAATACAAGGCTGATAAAAAAGCAGAGTCTGAAAAAATTGAACGTCAAATGCAACAGCAG
CTGGAAAGAGATGAAGAACTGAGAGAAACAGTAATCAAGATGCGAAGAAGAAGAAGAGAA
TTGCGACATAAATATGGAGGGGACGATGGGAATCTCGATTCAAGGACAAATAGTGACTCG
GGTGAAAATGAACCAAAGAGACGAAGGGATGATAGGGATAAAAAATCTACATCGAGCAGT
TCCGATGAATCGAGTAGACAAAAAAAGAGGGAAAGAAGTCGTAGTAGAAATCGCAGTCGT
TCAACATCGCGATATAAGAAAAAATACAGTCGCTCACCAGTTAGATATCGCAGATCGAGA
AGCTCAGGTAGGAATTATCGTCGTTCAAGGTCAAGATCGCGTGATTATCGTCGTTAA
>g9509.t1 Gene=g9509 Length=818
MWHEARKQEKKIKGMLVDYRKRADRRKEYYDKIKADPIRFMQVHGRKCKIHFEAVDSSDH
MMNFRIEGEDILIDRFDVRSHLDYISTPKKQEESTESEKISEEERQLNYERYKILASNEF
LGITEENFLKQIQIEEQFGSADKSDDKSKKKNSQATAAIGYTYEDSTATANIVPFSQQIL
SIEASSSSSRYEEFAKDYSDDSDIDMDVTIDVKKIGTQQAHELNNYGKKYGMHSNDLFSF
LTRDEDEKMSLKAMKEQEADKMLSGGRKSRRERRSQREKRILGRPLNSPPSYAAKEEEKE
KPLEDDDEDESDKSSRSKSPSVEKITFITSFGGEEELQPHPKISIPLKKTASQKLISNLR
KNETFSDMVKRNAEKLSHMNEYEKSKNSRRSRSRSSDHRRKRSRSRSSRRRYSSRSRSRS
RRRHDYSSRSRSRDRRSYRNRSSKSYSVSSYSSRDRRSSRSTSRRRYRSRHRSRNYRRTS
YRKSYSRHRSTSPEEKTYKKSTSRRRSDSRSRRKSSNRRHSTSRSFSSSSSSTTSSSSSS
SSSSSSSSKSSPVHRKSVETKSTKSSPLSSLPRSKSKSKSPLKLKRSSSREAELVKKESP
APIKRYYGRKRDDDSSSSLSIDSDDDDDKKIGSNESSTNDAYKVNRSAELKINMSKSTVG
PSVSNPREKLKKKMQILLNKQYKADKKAESEKIERQMQQQLERDEELRETVIKMRRRRRE
LRHKYGGDDGNLDSRTNSDSGENEPKRRRDDRDKKSTSSSSDESSRQKKRERSRSRNRSR
STSRYKKKYSRSPVRYRRSRSSGRNYRRSRSRSRDYRR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g9509.t1 | Coils | Coil | Coil | 679 | 710 | - |
| 23 | g9509.t1 | Coils | Coil | Coil | 816 | 818 | - |
| 12 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 255 | 818 | - |
| 14 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 255 | 281 | - |
| 18 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 364 | 390 | - |
| 21 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 391 | 438 | - |
| 16 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 442 | 456 | - |
| 11 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 459 | 485 | - |
| 9 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 487 | 504 | - |
| 17 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 505 | 520 | - |
| 19 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 521 | 553 | - |
| 7 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 562 | 577 | - |
| 15 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 584 | 634 | - |
| 10 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 635 | 664 | - |
| 8 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 666 | 714 | - |
| 20 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 739 | 770 | - |
| 13 | g9509.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 771 | 818 | - |
| 2 | g9509.t1 | PANTHER | PTHR13161:SF4 | CLK4-ASSOCIATING SERINE/ARGININE RICH PROTEIN | 1 | 508 | 1.4E-115 |
| 4 | g9509.t1 | PANTHER | PTHR13161 | SPLICING FACTOR SUPPRESSOR OF WHITE APRICOT | 1 | 508 | 1.4E-115 |
| 3 | g9509.t1 | PANTHER | PTHR13161:SF4 | CLK4-ASSOCIATING SERINE/ARGININE RICH PROTEIN | 480 | 718 | 1.4E-115 |
| 5 | g9509.t1 | PANTHER | PTHR13161 | SPLICING FACTOR SUPPRESSOR OF WHITE APRICOT | 480 | 718 | 1.4E-115 |
| 1 | g9509.t1 | Pfam | PF09750 | Alternative splicing regulator | 40 | 165 | 2.1E-32 |
| 6 | g9509.t1 | SMART | SM01141 | DRY_EERY_2 | 39 | 167 | 1.0E-44 |
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 K13168 (CLK4-associating serine/arginine rich protein)
Pathway
This gene does not belong to any 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.
