General information for g8114.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as U2 snRNP-associated SURP motif-containing protein.
Parent gene
- The parent gene g8114 is located on chr_2: 28645774..28647001 (- 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 | g8114 | g8114.t1 | TTS | g8114.t1 | 28643872 | 28643872 |
| chr_2 | g8114 | g8114.t1 | isoform | g8114.t1 | 28643978 | 28647001 |
| chr_2 | g8114 | g8114.t1 | exon | g8114.t1.exon1 | 28643978 | 28644080 |
| chr_2 | g8114 | g8114.t1 | cds | g8114.t1.CDS1 | 28643978 | 28644080 |
| chr_2 | g8114 | g8114.t1 | exon | g8114.t1.exon2 | 28644146 | 28644737 |
| chr_2 | g8114 | g8114.t1 | cds | g8114.t1.CDS2 | 28644146 | 28644737 |
| chr_2 | g8114 | g8114.t1 | exon | g8114.t1.exon3 | 28644804 | 28644878 |
| chr_2 | g8114 | g8114.t1 | cds | g8114.t1.CDS3 | 28644804 | 28644878 |
| chr_2 | g8114 | g8114.t1 | exon | g8114.t1.exon4 | 28644950 | 28645233 |
| chr_2 | g8114 | g8114.t1 | cds | g8114.t1.CDS4 | 28644950 | 28645233 |
| chr_2 | g8114 | g8114.t1 | exon | g8114.t1.exon5 | 28645291 | 28646350 |
| chr_2 | g8114 | g8114.t1 | cds | g8114.t1.CDS5 | 28645291 | 28646350 |
| chr_2 | g8114 | g8114.t1 | exon | g8114.t1.exon6 | 28646417 | 28646927 |
| chr_2 | g8114 | g8114.t1 | cds | g8114.t1.CDS6 | 28646417 | 28646927 |
| chr_2 | g8114 | g8114.t1 | exon | g8114.t1.exon7 | 28646996 | 28647001 |
| chr_2 | g8114 | g8114.t1 | cds | g8114.t1.CDS7 | 28646996 | 28647001 |
| chr_2 | g8114 | g8114.t1 | TSS | g8114.t1 | 28647098 | 28647098 |
Sequences
>g8114.t1 Gene=g8114 Length=2631
ATGAGTAAATTATCAAAAAGAGAATTAGAGGAAAAGAGGAGAAGAGAAATTGAAGAAGAA
AATGCAAAAGCTTTTGAGGATTTTTATGAAACATTTCAAAACACATCAAACTCAGCTGCT
TCAAAGGTTTGGATAAAAGCAGGAACATACGATGCTGGTTCAAGAAAAGAAGATACAAAG
GAGAAAGGAAAACTTTATAAGCCGACTCCAAAAGCTGGAACTTCTCATGACGATAACTCT
GCTTCTTCTGCTCAAGAATATGCAAGAATGCTAGCAACGTCAGATTCTCGTAAAGAAATA
ACACCTTTGGGCAAAAAGAAAGCTCAAGAGAAGAAAAAATCTAATTTAGAAATGTTTAAA
GAAGAACTCAAACAAATGCAAGAGGAACGTGAAGAGAGACATAAATATAAACATGCGGCG
AAATCAATGATGCAAATGCAAATTCACAGTGTTTTAGAACATCCTGAACCGATTTATCGT
GAAGTTCAAGAATCACAAGGAAGTTTTGATACAGGGGATCCAACAACTACCAATTTATAT
CTTGGTAATTTAAATCCTAAAATAACTGAGCAACAGTTAATGGAAATATTTGGAAAATAC
GGACCATTAGCAAGTGTTAAAATTATGTGGCCGAGATCTGATGAGGAAAAAGCTCGCGGT
AGAAATTGTGGATTTGTAGCATTTATGGCAAGAAAAGATGCTGAGCGTGCATTAAGGCGG
TTAGCAGGTAAAGATGTTATGGGTTATGAAATGAAACTTGGTTGGGGCAAAAGTGTCCCA
ATTATGACTCATCCGATTTATATTCCACCAAAATTACAAGAATATGCAATGCCACCACAA
AAATCAGGATTACCTTTTAATGCTCAACCACTTGGTGATGTTACAAATATCAATGTAGAT
GAACTTGATTTCAAATCATATTTAGTTGATGAAGAGAAAAAAAAGCAAATAGATGAGATT
TTATCAAAGACTATTGTAAAAGTAGTAATACCCACAGAGCGACCATTGCTCATGTTAATA
CATAGAATGATTGAATTTGTAATTCGAGAAGGACCAATTTTTGAATCTATGATAATGGCA
CGAGAACAAAATAATCCAAATTTTCGTTTTTTATTCGAATTCGACAGTGCAGCGCATATT
TATTATAGATGGAAATTATTTTCGTTGCTTCAAGGTGACACACCTTTAGAATGGAGTGAA
AAAGAATTTAGAATGTTTAAAAACTCATCAATTTGGCAACCACCAAAAGTATGTCAATTT
AGTCAAGGTATGCCAGAAGAATTAATTTCCGATGATGAATTGCTTGAACCTTGCAAAGGT
CAACTCTCTGTTGCACAAAGAAATCGACTTGAGGACTTGATCAGACATTTGACTCCAGAT
CGAAGTAAGATCGGAGATGCTATGGTTTTTTGTATTGAACATGCAGATGCTGCTGATGAA
ATTTGTGACTGTATTGCTGAATCATTGACAAATCCTCAAACAGCAATTCACAAAAAAATT
GCTAGAATTTATCTCGTTTCTGATATTCTTCATAATTGCACAGTAAAGGTTCAAAATGCG
AGCTTTTTTAGGAAATCAATGGAAAAAAATCTTATTGAAATGTTTAAAGGACTTCATGAT
AGCTACAAACTTTTAGAAAGTCGTTTGAAAGCAGAAGGTTTTAAAGTGAGAATTATGAAA
ATCTTTAGAACTTGGGAAGAATGGGCAGTTTATAGTCGTGATTTTTTGATAAAATTACAA
AATACATTTTTGGGTGTAGCAATTACTGAAAACACAGGCAACAGTGGTCATCAGTTATCA
GATAAAGAAGAAGACGAAGATCTTGATGGAATGCCTCTTGATGGTGCTGCACTTTTAAAA
GGAGCCCTGATGAGAGGAATTCGAACACCTGAACATTCAGAAAATGAAAATGAAGATGAC
ATCGATGGAGTACCATTGGTAGATGAAAATATTGATGGAGTTCCACTTTTGGCACCATCA
ACGACAGCAGCAGCAACAGATTCATCATCTGCAGGTTTTGTGAAGTCAAAATGGGAAGAA
TTGGATCCCGAGCAAGTAGCTCATCAAGCAATTACAACTTCTAAATGGGAATTTGATCCC
ATTGCTCCTGAACCACCAAAAATTTCTTCAATTTGTGATTATGGTAATAGTGAAAGCGAA
AGTAGCGAAAGTGAAACAGAAGAAAAACGCAGACGTTTAAGAGAGATTGAACTTAAAATT
TGTAAATATCAAGATGAACTAGAATCTGGTGAACGACAAATGAAAAGAGGATATACTGTG
CAAGAACAAGTTGAAAGTTATAGAAGAAAATTACTACGAAAATCTGAACGACATGATTCA
GATTCTCAATCAACTTCAGATCGCTATCAATCATCATCATCAAAACGAGAGCGAAGCAGG
AGAAGTAGAAGCTCATCAAATGAAAGACGAGTAAAAAAGTCTAGAAAATCATCGTCCTCT
GAGAGAGAGAAATATTATAGCAGTAGTTCAAAAATATCAAAATCACCATCATCCTCATCA
AAATCAAAACATCCCAAACGAAGTGGCAGAAGTAGAAGCAAAGACAGCCTCTCGAATTCA
CCATCGTATTCGTCATCAAGAAAGTCACACAAGTCCAAATATAAATATTAA
>g8114.t1 Gene=g8114 Length=876
MSKLSKRELEEKRRREIEEENAKAFEDFYETFQNTSNSAASKVWIKAGTYDAGSRKEDTK
EKGKLYKPTPKAGTSHDDNSASSAQEYARMLATSDSRKEITPLGKKKAQEKKKSNLEMFK
EELKQMQEEREERHKYKHAAKSMMQMQIHSVLEHPEPIYREVQESQGSFDTGDPTTTNLY
LGNLNPKITEQQLMEIFGKYGPLASVKIMWPRSDEEKARGRNCGFVAFMARKDAERALRR
LAGKDVMGYEMKLGWGKSVPIMTHPIYIPPKLQEYAMPPQKSGLPFNAQPLGDVTNINVD
ELDFKSYLVDEEKKKQIDEILSKTIVKVVIPTERPLLMLIHRMIEFVIREGPIFESMIMA
REQNNPNFRFLFEFDSAAHIYYRWKLFSLLQGDTPLEWSEKEFRMFKNSSIWQPPKVCQF
SQGMPEELISDDELLEPCKGQLSVAQRNRLEDLIRHLTPDRSKIGDAMVFCIEHADAADE
ICDCIAESLTNPQTAIHKKIARIYLVSDILHNCTVKVQNASFFRKSMEKNLIEMFKGLHD
SYKLLESRLKAEGFKVRIMKIFRTWEEWAVYSRDFLIKLQNTFLGVAITENTGNSGHQLS
DKEEDEDLDGMPLDGAALLKGALMRGIRTPEHSENENEDDIDGVPLVDENIDGVPLLAPS
TTAAATDSSSAGFVKSKWEELDPEQVAHQAITTSKWEFDPIAPEPPKISSICDYGNSESE
SSESETEEKRRRLREIELKICKYQDELESGERQMKRGYTVQEQVESYRRKLLRKSERHDS
DSQSTSDRYQSSSSKRERSRRSRSSSNERRVKKSRKSSSSEREKYYSSSSKISKSPSSSS
KSKHPKRSGRSRSKDSLSNSPSYSSSRKSHKSKYKY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g8114.t1 | CDD | cd12223 | RRM_SR140 | 176 | 259 | 1.53837E-53 |
| 14 | g8114.t1 | Coils | Coil | Coil | 7 | 27 | - |
| 13 | g8114.t1 | Coils | Coil | Coil | 106 | 129 | - |
| 12 | g8114.t1 | Coils | Coil | Coil | 719 | 739 | - |
| 11 | g8114.t1 | Gene3D | G3DSA:1.10.10.790 | - | 332 | 393 | 1.9E-18 |
| 10 | g8114.t1 | Gene3D | G3DSA:1.25.40.90 | - | 442 | 585 | 1.4E-34 |
| 25 | g8114.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 49 | 84 | - |
| 22 | g8114.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 51 | 67 | - |
| 20 | g8114.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 697 | 731 | - |
| 24 | g8114.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 744 | 876 | - |
| 21 | g8114.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 762 | 784 | - |
| 23 | g8114.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 823 | 839 | - |
| 5 | g8114.t1 | PANTHER | PTHR23140 | RNA PROCESSING PROTEIN LD23810P | 5 | 794 | 3.1E-230 |
| 6 | g8114.t1 | PANTHER | PTHR23140:SF0 | U2 SNRNP-ASSOCIATED SURP MOTIF-CONTAINING PROTEIN | 5 | 794 | 3.1E-230 |
| 4 | g8114.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 179 | 251 | 5.1E-14 |
| 2 | g8114.t1 | Pfam | PF01805 | Surp module | 338 | 388 | 3.5E-18 |
| 3 | g8114.t1 | Pfam | PF04818 | CID domain | 450 | 578 | 6.2E-12 |
| 1 | g8114.t1 | Pfam | PF08312 | cwf21 domain | 728 | 774 | 3.7E-7 |
| 26 | g8114.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 177 | 258 | 16.654 |
| 28 | g8114.t1 | ProSiteProfiles | PS50128 | SURP motif repeat profile. | 339 | 382 | 13.964 |
| 27 | g8114.t1 | ProSiteProfiles | PS51391 | CID domain profile. | 442 | 587 | 38.294 |
| 19 | g8114.t1 | SMART | SM00360 | rrm1_1 | 178 | 254 | 7.4E-17 |
| 16 | g8114.t1 | SMART | SM00648 | surpneu2 | 337 | 391 | 2.4E-16 |
| 17 | g8114.t1 | SMART | SM00582 | 558neu5 | 445 | 584 | 3.4E-31 |
| 18 | g8114.t1 | SMART | SM01115 | cwf21_2 | 725 | 776 | 6.7E-11 |
| 7 | g8114.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 165 | 260 | 4.97E-21 |
| 8 | g8114.t1 | SUPERFAMILY | SSF109905 | Surp module (SWAP domain) | 321 | 395 | 1.7E-20 |
| 9 | g8114.t1 | SUPERFAMILY | SSF48464 | ENTH/VHS domain | 448 | 582 | 3.14E-9 |
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:0003723 | RNA binding | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12842 (U2-associated protein SR140)
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.
