Sequence
atgc intronic sequence ATGC exonic sequencegttttaaggctcatctactacatttactcctcaagtccatattgatagtttatttctctaaacgattgaggtgtaactgtagATCGCTCCTATCATACACGAATGGACCTATGATGCTATGTGCCATGATTTGCTTGACATGGAGGGGAATAAACATGTCATTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G02010.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G02010.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g04450.1 (Oryza sativa), 3'ss of exon 9
-------------------gttttaa-ggctcatctac---tacatttactcctcaagtccatattgatagtttatttctctaaacgattgaggtgtaactgta--gATCGCTCCTATCATACACGAATGGACCTATGATGCTATGTGCCATGATTTGCTTGACATGGAGGGGAATAAACATGTCATTGAG
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gtgctgaaggataacttatgtttcaataacttgtcagtgtagaagtatattgaagaaattca-gtatctttcctactgcttacaataatttccgtatgtctgcaaagATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTTGAAATGGATGGCCAAAAATACATATATGAG
upper sequence: AT1G02010.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G830776_T02 (Zea mays), 3'ss of exon 10
---------------------------gttttaagg-ctcatctactacatttactcctca-agtccatattgatagtttatttctctaaacgattgaggtgtaactgt--agATCGCTCCTATCATACACGAATGGACCTATGATGCTATGTGCCATGATTTGCTTGACATGGAGGGGAATAAACATGTCATTGAG
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gtgctaaagcatacactggatgctaaaactttaagaatttgttcacttaaaatacagcaaagaacttcaatttattcattacagcttacaacaatttca-tatgactgcaaagATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAG
upper sequence: AT1G02010.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G34340.1 (Glycine max), 3'ss of exon 4
gttttaaggctcatctactacatttactcctcaagtccatattgatagttt---atttctctaaacg-attgaggtgtaactgtagATCGCTCCTATCATACACGAATGGACCTATGATGCTATGTGCCATGATTTGCTTGACATGGAGGGGAATAAACATGTCATTGAG
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--gttaaaaatgtctcttcactatgaatatgaatgtctccttttatagctctcaattttgatgactgtattgaatctgcaccacagATTGCACCTGTCATTCATGAATGGACCTATGATGCTATGTGCCATGATTTGTTGAATATGGATGGAGATAAATATATGCATGAG
upper sequence: AT1G02010.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G02740.1 (Glycine max), 3'ss of exon 9
gttttaaggctcatctactacatttactcctcaagtccatattgatagtttatttctctaaacgattgaggtgtaactgta-----gATCGCTCCTATCATACACGAATGGACCTATGATGCTATGTGCCATGATTTGCTTGACATGGAGGGGAATAAACATGTCATTGAG
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gttgttaaaaatgtct-cttcacta--tatgaatgtctccttttatagctctcaccttttgatgactgtgttgaatctgcaccacagATTGCACCTGTCATTCATGAATGGACCTATGATGCTATGTGCCATGATTTGTTGACTATGGATGGAGATAAATATATGCATGAG
upper sequence: AT1G02010.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv15s0048g00970.t01 (Vitis vinifera), 3'ss of exon 8
gttttaaggctcatctactacatttactcctcaagtccatattgatagtttatttctctaaac--gattgaggtgtaactgtagATCGCTCCTATCATACACGAATGGACCTATGATGCTATGTGCCATGATTTGCTTGACATGGAGGGGAATAAACATGTCATTGAG
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gttattat-ctattttcctgttgtgaatttattgccatattttctcagttagatttattgaatatgatgattttgcatgtttagATAGCTCCTGTCATACATGAATGGACCTATGATGCCATGTGCCATGATTTACTGGAGATGGATGGAAATAAATATGTACACGAG
upper sequence: AT1G02010.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv15s0045g00060.t01 (Vitis vinifera), 3'ss of exon 1
gttttaaggctcatctactacatttactcctcaagtccatattgatagtttatttctctaaac--gattgaggtgtaactgtagATCGCTCCTATCATACACGAATGGACCTATGATGCTATGTGCCATGATTTGCTTGACATGGAGGGGAATAAACATGTCATTGAG
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gttattat-ctattttcctgttgtgaatttattgccatattttctcagttagatttattgaatatgatgattttgcatgtttagATAGCTCCTGTCATACATGAATGGACCTATGATGCCATGTGCCATGATTTACTGGATATGGATGGAAATAAATATGTACACGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctcaagtccatattgatagtttatttctctaaacgattgaggtgtaactgtagATCGCTCCTATCATACACGAATGGACCTATGATGCTATGTGCCATGATTTGCTTGACATGGAGGGGAATAAACATGTCATTGAG
gtgtaac putative branch site (score: 3)
atattgatagtttatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttaaggctcatctactacatttactcctcaagtccatattgatagtttatttctctaaacgattgaggtgtaactgtagATCGCTCCTATCATACACGAATGGACCTATGATGCTATGTGCCATGATTTGCTTGACATGGAGGGGAATAAACATGTCATTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG