Sequence
atgc intronic sequence ATGC exonic sequence...gaatcatagatttgttgttagctgtggcatgatgaatcagaattgaagaaatgatttttgaatctctcttttttttttccaattttgtgattaatgacagGTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G17060.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G113995_T03 (Zea mays), 3'ss of exon 1
---gaatcatagatttgttg----ttagctgtggcatgatgaatcagaattgaagaaatgatttttgaatctctcttttttttttccaattttgtgattaat-gacagGTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTG
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gtctgctcatatttttgccgcgatttttctttcgctatttagttgtactttctacgaactgcctgtatgtatcattttgttgattgtggttttgtgcttgcttgttagGTTGTGATGCTTGGTCTGGATGCTGCCGGTAAAACCACCATATTGTACAAGCTGCATATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG
upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 2
gaatcatagatttgttgttagctgtggcatgatgaatcagaattgaagaaatgatttttgaatctctcttttttttttccaattttgtgattaatgacagGTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTG
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-----gtaactttctgcttgattgttaaatgttaatttttac---actcaattattattaattttattatttccttgatctgtttgtt---------cagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG
upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G09790.2 (Glycine max), 3'ss of exon 1
gaatcatagatttgttgttagctgtggcatgatgaatcagaattgaagaaatgatttttgaatctctcttttttttttccaattttgtg-attaatgacagGTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTG
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tgttcgttaatac-ttgtgtttcttattctcatcatccatcttctaatcattgattcttgatctatgcacgagtttccgtacttacatttgttgggtttagGTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG
upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G02110.1 (Glycine max), 3'ss of exon 1
----gaatcatagatttgttgttagctgtggcatgatgaatcagaattgaagaaatgatttttgaatctctcttttttttttccaattttgtgattaatgacagGTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTG
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ttgtttttcttagtctcatcatccatcttctaaccatagatccttgatctttgcatgagtttccgtacttactttttttttttacattt----gttgggattagGTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG
upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 2
gaatcatagatttgttgttagctgtggcatgatgaatcagaattgaagaaatgatttttgaatctctcttttttttttccaattttgtgattaatgacagGTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTG
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-----gtaactttctgcttgcttgttaaacgttaatt-----ttttacactcaatttattattaactttattatttccttgatctgtttgtt-----cagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG
upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 1
gaatcatagatttgttgttagctgtggcatgatgaatcagaattgaagaaatgatttttgaatctctcttttttttttc-caattttgtgattaatgacagGTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTG
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tattcttgagtttatgcctgtattcttaatatttattcatgatttctcta-tgtccttcgagcttattttcttatttaaattattaattgagttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAATTGCACATTGGAGAAGTTTTGTCCACTGTTCCCACAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagaaatgatttttgaatctctcttttttttttccaattttgtgattaatgacagGTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTG
gattaat putative branch site (score: 3)
ttttttttttccaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatcatagatttgttgttagctgtggcatgatgaatcagaattgaagaaatgatttttgaatctctcttttttttttccaattttgtgattaatgacagGTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
-aatcata
- - - - gatttgt
- - - - - - - - - - - - - - - - - -atcagaa
- - - - - - - - - - - - - - - - - - - - - - -aagaaat