Sequence
atgc intronic sequence ATGC exonic sequencegtttattcaaattcacttttttctactttatagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAATTTCAGCTCACAGTCAATGTCGCCGCTCTCGTAATTAATGTTGTAGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57110.1 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25
gtttattcaaattcacttttttctacttt---atagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAATTTCAGCTCACAGTCAATGTCGCCGCTCTCGTAATTAATGTTGTAGCTG
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---------------gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttga---acactgattgtaca---atgagaggtttatatagaagtgagg-tgcatttaatat---tgaagc----acaactgatgatgacaattgtgtttctccatggt--------tgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG
upper sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 28
gtttattcaaattcacttttttctactttatagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAATTTCAGCTCACAGTCAATGTCGCCGCTCTCGTAATTAATGTTGTAGCTG
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---------------------------------------------------------------------------------------cgagtttgttgatcaaagtttcccttcgatgcctaca-----gcatttggataagttgaa---gaagctgggatctttgtaactgttgatttctcttgttgcat-----ttagGTTGTCAGATGGGGACGATCTGTATATGCAAATATACAGAAATTCATCCAGTTTCAGCTCACAGTTAATGTTGCAGCTCTAATAATTAATGTCGTGGCAG
upper sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 27
gttt-attcaaattcacttttttctactttatagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAATTTCAGCTCACAGTCAATGTCGCCGCTCTCGTAATTAATGTTGTAGCTG
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gttcgattcgatcagtcattcctctaatctagagttcctcatgttc-----agctttgtaacccaatcgcatagccgttgta-------tactttgcacgtccgt---tagtgaaggta--cttactttttagttaatagttagtaggttttctctggggatgtacttatgtctgacgtttctgt----tctgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAATTTCAACTGACTGTCAATGTTACGGCTCTTACCATCAATTTTGTCGCAT
upper sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
gtttattcaaattcacttttttctactttatagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAATTTCAGCTCACAGTCAATGTCGCCGCTCTCGTAATTAATGTTGTAGCTG
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-------------------------------------------------------------------------------------------------------------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
upper sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 23
gtttattcaaattcacttttttctactttatagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAATTTCAGCTCACAGTCAATGTCGCCGCTCTCGTAATTAATGTTGTAGCTG
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-------------------------------------------------------------------------------------------------------------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTAGTTGCGCTGGTTCTCAACGTCGTGGCCGMapped 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|86081055|gb|DR376812.1|DR376812EST: AGAGTTCGGACATCATCATCTTGGATGACAACTTTGCTTCAGTTGTCAAG GTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAA
genomic: AGAGTTCGGACATCATCATCTTGGATGACAACTTTGCTTCAGTTGTCAAGgtttattcaa ... tattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAATTTCAGCTCACAGTCAATGTCGCCGCTCTCGTAATTAATGTTGTAGCTG
ccttaat putative branch site (score: 4)
ttaatttgtggtgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttattcaaattcacttttttctactttatagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAATTTCAGCTCACAGTCAATGTCGCCGCTCTCGTAATTAATGTTGTAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA