Sequence
atgc intronic sequence ATGC exonic sequencegtacctacaatccagagcaaattttgcttgagctttgtgcacaagtacaatgcgaccacaaaagtttctaatgggtttttaaaattctaattcagAACCAAATCCTTACATGGGGCATCTAGCTTGGGGTGATGCTTTTGTGGTGACAGCAGATTCAGTCAGTCTGATAAGCGAAGCTTGTAGCACCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22350.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22350.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g33230.1 (Oryza sativa), 3'ss of exon 7
gtacctacaatccagagc-aaattttgcttga---gctttgtgcacaa-gtacaatgcgaccacaaaagtttctaatgggtttttaaaattctaattcagAACCAAATCCTTACATGGGGCATCTAGCTTGGGGTGATGCTTTTGTGGTGACAGCAGATTCAGTCAGTCTGATAAGCGAAGCTTGTAGCACCGG
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gtagatgaaatataacactaagttattcatgatgtaatatatttattatgcatgttgttacatttgtaagttgtaacaagttgattttatttt--tgcagAACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAACAGCTGATTCTATAAGTATGTTAAGTGAGGCTTGTAGCACAGG
upper sequence: AT5G22350.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G39140.1 (Glycine max), 3'ss of exon 7
----gtacctac---aatccagagcaaattttgcttgagctttgtgcacaagtacaatgcgaccacaaaagtttctaatgggtttttaaaattctaatt-cagAACCAAATCCTTACATGGGGCATCTAGCTTGGGGTGATGCTTTTGTGGTGACAGCAGATTCAGTCAGTCTGATAAGCGAAGCTTGTAGCACCGG
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gtaaatatttattcagatttagattagattat--ttaatcagattttggaagtttgttttgacttacaatgtggttaatccctgtcactaacacaattttcagAACCAAACCCACATATGGGGCATCTGGCTTGGGCTGATGCATTTGTTGTCACAGCAGATTCAGTTAGCATGATAAGTGAAGCTTGCAGCACCGG
upper sequence: AT5G22350.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G31170.1 (Glycine max), 3'ss of exon 7
----gtacctac---aatccagagcaaatt-ttgcttgagctttgtgcacaagtacaatgcgaccacaaaagttt--ctaatgggtttttaaaattctaatt-cagAACCAAATCCTTACATGGGGCATCTAGCTTGGGGTGATGCTTTTGTGGTGACAGCAGATTCAGTCAGTCTGATAAGCGAAGCTTGTAGCACCGG
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gtaaatatttatccaggtttagaatagattatttaatcagatttgt---taaatttgttttaacagtcagaatgtggttaatccatgtcactaacacaattttcagAACCAAACCCACAAATGGGGCATCTAGCTTGGGCCGATGCATTTGTTGTCACAGCAGATTCAGTTAGCATGATAAGTGAAGCTTGCAGCACTGG
upper sequence: AT5G22350.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G18750.1 (Glycine max), 3'ss of exon 7
gtacctacaatccagagcaaattttgcttgagctttgtgcacaagtacaatgcgaccacaaaagtttctaatgggtttttaaaattctaattcagAACCAAATCCTTACATGGGGCATCTAGCTTGGGGTGATGCTTTTGTGGTGACAGCAGATTCAGTCAGTCTGATAAGCGAAGCTTGTAGCACCGG
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----gtaaaaatttgttccagttttgattcagatattta---aaatatggttcaacagataaacttgacagtaa-----tacaact----ttcagGACATAACCGGCACATGGGCCATTTAGCTTGGGCCGATGCATTTGTTGTCACAGCAGATTCAGTTAGCATGATAAGTGAAGCATGCAGCACTGG
upper sequence: AT5G22350.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0080g00830.t01 (Vitis vinifera), 3'ss of exon 7
gtacctacaatccagagcaaattttgcttgagctttgtgcacaagtacaatgcgaccacaaaagtttctaatgggtttttaaaattctaattca--gAACCAAATCCTTACATGGGGCATCTAGCTTGGGGTGATGCTTTTGTGGTGACAGCAGATTCAGTCAGTCTGATAAGCGAAGCTTGTAGCACCGG
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gtaatcttagtc--gatttgattctgaatgaa-tgaataaaatggaactaaaccatgatatgatcatctaatttatatgttgtgtgataatctatagAACCAAATCCACACATGGGACATCTAGCTTGGGCTGATGCTTTTGTTGTCACAGCAGATTCAGTGAGTATGATAAGTGAGGCTTGCAGCACAGGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116460255|gb|EG502847.1|EG502847EST: CTTCAAAGAACTTGGAGATAACCCCAAAGTTTACATATGGAATGGCCAAG AACCAAATCCTTACATGGGGCATCTAGCTTGGGGTGATGCTTTTGTGGTGA
genomic: CTTCAAAGAACTTGGAGATAACCCCAAAGTTTACATATGGAATGGCCAAGgtacctacaa ... tctaattcagAACCAAATCCTTACATGGGGCATCTAGCTTGGGGTGATGCTTTTGTGGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaagtacaatgcgaccacaaaagtttctaatgggtttttaaaattctaattcagAACCAAATCCTTACATGGGGCATCTAGCTTGGGGTGATGCTTTTGTGGTGACAGCAGATTCAGTCAGTCTGATAAGCGAAGCTTGTAGCACCGG
ttctaat putative branch site (score: 2)
tttttaaaattctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctacaatccagagcaaattttgcttgagctttgtgcacaagtacaatgcgaccacaaaagtttctaatgggtttttaaaattctaattcagAACCAAATCCTTACATGGGGCATCTAGCTTGGGGTGATGCTTTTGTGGTGACAGCAGATTCAGTCAGTCTGATAAGCGAAGCTTGTAGCACCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT