General information for g10583.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-splicing factor syf1-like protein.
Parent gene
- The parent gene g10583 is located on chr_1: 10529911..10530557 (+ 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 | g10583 | g10583.t1 | TSS | g10583.t1 | 10527585 | 10527585 |
| chr_1 | g10583 | g10583.t1 | isoform | g10583.t1 | 10527825 | 10530557 |
| chr_1 | g10583 | g10583.t1 | exon | g10583.t1.exon1 | 10527825 | 10527878 |
| chr_1 | g10583 | g10583.t1 | cds | g10583.t1.CDS1 | 10527825 | 10527878 |
| chr_1 | g10583 | g10583.t1 | exon | g10583.t1.exon2 | 10527965 | 10528125 |
| chr_1 | g10583 | g10583.t1 | cds | g10583.t1.CDS2 | 10527965 | 10528125 |
| chr_1 | g10583 | g10583.t1 | exon | g10583.t1.exon3 | 10528187 | 10530557 |
| chr_1 | g10583 | g10583.t1 | cds | g10583.t1.CDS3 | 10528187 | 10530557 |
| chr_1 | g10583 | g10583.t1 | TTS | g10583.t1 | 10530604 | 10530604 |
Sequences
>g10583.t1 Gene=g10583 Length=2586
ATGCCTATATTAAGTGAATTTAAAGAGAATAACATGGATATTGATTTAGATCTTAAAGAC
GATGATCTTCCGTATGAAGAAGAAATTTTGCGAAATGCATATTCGGTGAAGCATTGGATG
CGTTATATTGAGCACAAAAGACATGCATCGAAACATATTATAAATCAGATCTATGAACGT
GCACTAAAACAGCTTCCTGCTTCATATAAATTATGGTACAATTATCTCAAATTGCGAAAG
AAACAAGTTAGAGGTAAAAGTATTCAAGATGAAGAGCTAGAAGATGTCAATAATGCATTC
GAAAGAGTTTTAGTTTTCATGCATAAAATGCCAAGAATATGGATTGATTATCTCTCATTT
CTCTCTAATCAATGCAAAATCACAAGAATTCGTCATACATTTGATCGTGGATTGCGTGCA
CTTCCTGTTACTCAACATAATCGCATTTGGCCACTTTATCTTGAGTTTTTGAATATGTAT
GATATTCCTGAAACGGGCGTTAGAGTATACAGACGATATTTAAAGTTATGCCCGGAAGAT
GCAGAAGAATTTATCAATTATTTGGTAAATAACAATCGACTTGATGAAGCCGCTCAGCAA
CTCGTAAAAATTGTTGATAATGAGCGTTTTGTCTCTAAATATGGCAAATCAAATCATCAA
CTTTGGAATGAACTTTGTGAGTTGATATCGAAAAATCCACAAAAAATTACCTCACTTAAT
GTTGATGCCATCATAAGAAGCGGATTACGTCGATATACAGATCAATTAGGACATTTATGG
AATTCGCTAGCTGATTATTATGTACGTAGTGGTTTATTTGAAAGAGCACGTGATATATAC
GAAGAAGCAATTGAGACTGTTACTACTGTTCGTGATTTTTCACAAGTTTTTGATGCTTAT
GCACAATTTGAAGAGCTTAGTTTGAGTAAATTGATGGAAGAAATAAATGCAAAAGAGACA
CCTTCACAAGATGATGACATTGAAATTGATTTACGAATGGCACGCTTTGAGAATCTAATG
GAAAGACGATTAGCGCTGTTGAATAGTGTTTTGTTGAGACAAAATCCACATAATGTCCAA
GAATGGCATAATCGTGTAAAACTATTTGAAGGAAATCCATTGGAAATTATTAAAATTTAT
ACTGAAGCAGTTCAAACTGTACAGCCTAAACTTGCAACAGGAAAACTTTACACTTTGTGG
GTAGAGTTTGCAAAGTTTTATGAAGAAAATGATCAAATTGATGATGCTCGAACAGTTTTT
GAGAAAGCAACTCAAGTAGAATATGCAAAAGTAGACGAACTTGCTGCTGTTTGGTGTGAA
TGGGCTGAAATGGAAATTCGCAAAGACAATTACAAGAATGCTCTTGATTTGATGTATAAG
GCAACTATCATACCAAAAAATAAAATTTCATATACAGATGAATCGGAAACAGTTCAAGCA
AGATTACATAAAAGTCTTAAACTTTGGTCAATGTATGCTGATTTAGAAGAGAGTTTTGGG
ACATTTCAAAGTTGTAAAAGTGTATATGATAGAATCATTGATTTAAGGATATGCACACCA
CAAATTATAATCAACTATGGTATGTTTTTAGAAGAGAATAAATATTTTGAAGAAGCCTTT
AGAGCATACGAAAAAGGAATAGCTCTTTTTAAATGGCCAAATGTATATGATATTTGGAAT
ATTTACTTGACTAAATTCTTAGCGCGATATGGTGGGAAACAATTGGAAAGAGCACGTGAC
CTTTTCGAACAGTGTATTGAAAATTGTCCACCAGATTTGGTTAAAACTTTCTATCTTCTC
TATGCAAAATTAGAAGAAGAACATGGTCTTGCGAGACATGTTATGACAGTTTATGAGAGA
GCTGTAAGTGCTGTTCAAGAGAGTGACATGTATGAAATGTTTAATTTATACATTAAAAAA
GCTGCAGAAATTTATGGAATTCCACGAACAAGACCTATTTATGAAAAAGCTATTGAAATG
TTGCCTGAAACAAAAGCACGTGAAATGTGCATTCGATTTGCAGAGATGGAAACAAAACTT
GGAGAAATTGATAGAGCGCGTGTTATTTATTCACATTGCAGTCAAATGTGTGATCCTCGA
ATCACTCAAGATTTTTGGCAAAAATGGAAAGATTTTGAAATTCGTCATGGTAATGAAGAA
ACGATGAGAGAAATGTTGAGAATTAAACGAAGCGTACAAGCAACTTATAACACTCAAGTT
AACATGATGTCCGCACAAATACCATCATCAATTGAACCGGTAAAAAGTGCAATGCAAGCG
CTTGAAGCGAAAGCAATCGAGACAAATTATAAACAAAATTTGGTATCTGCCGCTGTCGGT
GCAAATATTGCATTTGTACGAGGAGAAGTTCAGGGAGGTGATTATAAGAAGAAGCAACAA
GATGATGGTGCAGTTTATAATCCAGATGAAATTGACATTGATATGGATGACGACAATAGT
GAGGAATCTGATGAGGAAAATGATACAGAAGAAGGAAAAGAATTGAAGAATATACCAATT
GAGAAGCAACCAGTTCCTGCGACCGTTTTTGGTGGACTGAAAAAAAAAGATTCGGATTCT
GAATAA
>g10583.t1 Gene=g10583 Length=861
MPILSEFKENNMDIDLDLKDDDLPYEEEILRNAYSVKHWMRYIEHKRHASKHIINQIYER
ALKQLPASYKLWYNYLKLRKKQVRGKSIQDEELEDVNNAFERVLVFMHKMPRIWIDYLSF
LSNQCKITRIRHTFDRGLRALPVTQHNRIWPLYLEFLNMYDIPETGVRVYRRYLKLCPED
AEEFINYLVNNNRLDEAAQQLVKIVDNERFVSKYGKSNHQLWNELCELISKNPQKITSLN
VDAIIRSGLRRYTDQLGHLWNSLADYYVRSGLFERARDIYEEAIETVTTVRDFSQVFDAY
AQFEELSLSKLMEEINAKETPSQDDDIEIDLRMARFENLMERRLALLNSVLLRQNPHNVQ
EWHNRVKLFEGNPLEIIKIYTEAVQTVQPKLATGKLYTLWVEFAKFYEENDQIDDARTVF
EKATQVEYAKVDELAAVWCEWAEMEIRKDNYKNALDLMYKATIIPKNKISYTDESETVQA
RLHKSLKLWSMYADLEESFGTFQSCKSVYDRIIDLRICTPQIIINYGMFLEENKYFEEAF
RAYEKGIALFKWPNVYDIWNIYLTKFLARYGGKQLERARDLFEQCIENCPPDLVKTFYLL
YAKLEEEHGLARHVMTVYERAVSAVQESDMYEMFNLYIKKAAEIYGIPRTRPIYEKAIEM
LPETKAREMCIRFAEMETKLGEIDRARVIYSHCSQMCDPRITQDFWQKWKDFEIRHGNEE
TMREMLRIKRSVQATYNTQVNMMSAQIPSSIEPVKSAMQALEAKAIETNYKQNLVSAAVG
ANIAFVRGEVQGGDYKKKQQDDGAVYNPDEIDIDMDDDNSEESDEENDTEEGKELKNIPI
EKQPVPATVFGGLKKKDSDSE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g10583.t1 | Gene3D | G3DSA:1.25.40.10 | - | 513 | 767 | 3.6E-25 |
| 21 | g10583.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 794 | 861 | - |
| 20 | g10583.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 807 | 829 | - |
| 2 | g10583.t1 | PANTHER | PTHR11246:SF5 | PRE-MRNA-SPLICING FACTOR SYF1 | 18 | 813 | 0.0 |
| 3 | g10583.t1 | PANTHER | PTHR11246 | PRE-MRNA SPLICING FACTOR | 18 | 813 | 0.0 |
| 1 | g10583.t1 | Pfam | PF13181 | Tetratricopeptide repeat | 259 | 285 | 0.14 |
| 15 | g10583.t1 | SMART | SM00386 | hat_new_1 | 49 | 81 | 0.28 |
| 18 | g10583.t1 | SMART | SM00386 | hat_new_1 | 91 | 123 | 0.96 |
| 12 | g10583.t1 | SMART | SM00386 | hat_new_1 | 125 | 159 | 6.8 |
| 14 | g10583.t1 | SMART | SM00386 | hat_new_1 | 271 | 306 | 0.011 |
| 19 | g10583.t1 | SMART | SM00386 | hat_new_1 | 411 | 447 | 13.0 |
| 17 | g10583.t1 | SMART | SM00386 | hat_new_1 | 470 | 498 | 360.0 |
| 13 | g10583.t1 | SMART | SM00386 | hat_new_1 | 500 | 532 | 75.0 |
| 10 | g10583.t1 | SMART | SM00386 | hat_new_1 | 534 | 568 | 8.7 |
| 16 | g10583.t1 | SMART | SM00386 | hat_new_1 | 573 | 607 | 2.4E-6 |
| 9 | g10583.t1 | SMART | SM00386 | hat_new_1 | 609 | 643 | 230.0 |
| 11 | g10583.t1 | SMART | SM00386 | hat_new_1 | 645 | 679 | 140.0 |
| 8 | g10583.t1 | SMART | SM00386 | hat_new_1 | 681 | 715 | 0.15 |
| 4 | g10583.t1 | SUPERFAMILY | SSF48452 | TPR-like | 26 | 82 | 4.46E-9 |
| 7 | g10583.t1 | SUPERFAMILY | SSF48452 | TPR-like | 88 | 489 | 6.5E-31 |
| 6 | g10583.t1 | SUPERFAMILY | SSF48452 | TPR-like | 482 | 643 | 3.67E-21 |
| 5 | g10583.t1 | SUPERFAMILY | SSF48452 | TPR-like | 649 | 727 | 3.16E-12 |
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:0006396 | RNA processing | BP |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12867 (pre-mRNA-splicing factor SYF1)
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.
