Sequence
atgc intronic sequence ATGC exonic sequencegttaatcttgaagctaattatgaaaccaatgttgattttatcttcatgatcgctaatcacgaaaccatgcattcttgagtttttcttgcatgaagctgtgtttgttgtaatgcagGAAGGGACATCGAATTACTTCAAAAGATTGATGCTCATTCTTTGCTATTTGATAGTCGCTGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55720.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G44920.1 (Glycine max), 3'ss of exon 9
gttaatcttgaagctaattatgaaaccaatgttgattttatcttcatgatcgctaatcacg-aaaccatgcattcttgagtttttcttgcatgaagctgtgtttgttgtaatgcagGAAGGGACATCGAATTACTTCAAAAGATTGATGCTCATTCTTTGCTATTTGATAGTCGCTGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG--
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gtttgtattcaaagataaaagaatgaaaatgaaaattatgctattaggaacccaaaacatgtagacaatgacatatgttaacattgtgacattaatttat-tatgcatt--tgcagGAAGGAACTGCCAATTACTTCAAAGGACTACTGCTTATTCTTTGCTATCTGATAGTGGCTGCCAGTTTTTATGTACATTTAGATTCCTCTCAATAA
upper sequence: AT1G55720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G44910.1 (Glycine max), 3'ss of exon 9
-------gttaatcttgaagctaattatgaaaccaatgttgattttatcttcatgatcgctaatcacgaaaccatgcat-tcttgagtttttcttgcatgaagctg-tgtttgttgtaa---tgcagGAAGGGACATCGAATTACTTCAAAAGATTGATGCTCATTCTTTGCTATTTGATAGTCGCTGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG------
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gtttgtattcaaacataaaaaaaagaatgaaaattaaaagtatggtattacgaatgttaacaatgacttgattattagtatggtgaagactgaagagacaacactgacatttattatgcatttgcagGAAGGAACTGCTAATTACTTCAAAGGACTAATGCTTATTCTTTGCTATCTGATAGTGGCAGCCAGTTTTTATGTACATGTAGATTCCTCTCAATAAGTTA
upper sequence: AT1G55720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv19s0015g01320.t01 (Vitis vinifera), 3'ss of exon 10
gttaatcttgaagctaattatg-aaaccaatgttgattttatcttcatgatcgctaatcacgaaaccatgcattcttgagt--ttttcttgcatgaagctgtgt-------ttgttgtaat-gcagGAAGGGACATCGAATTACTTCAAAAGATTGATGCTCATTCTTTGCTATTTGATAGTCGCTGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG---
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gtttgtattcaatgaaggaacacagatctatat-actttgatagtggtgtcttgtagatattcatcattatttctctgtttggttatttcacaataacttacatattcctcttgttttgtttgcagGAAGGCACTTCTAATTACTTTAAAGGACTAATGCTCATTCTTTGCTATCTAATAGTTGCAGCAAGTTTCTTTGTACATGTCGATCCTACTTTAGTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaccatgcattcttgagtttttcttgcatgaagctgtgtttgttgtaatgcagGAAGGGACATCGAATTACTTCAAAAGATTGATGCTCATTCTTTGCTATTTGATAGTCGCTGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG
tttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatcttgaagctaattatgaaaccaatgttgattttatcttcatgatcgctaatcacgaaaccatgcattcttgagtttttcttgcatgaagctgtgtttgttgtaatgcagGAAGGGACATCGAATTACTTCAAAAGATTGATGCTCATTCTTTGCTATTTGATAGTCGCTGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA