Sequence
atgc intronic sequence ATGC exonic sequencegtttgcatagatctttcttagagatcatctaaaagtgcaagctctagaaattgatattgcataagaatcatcaaacttgcaatccaagaaatccaaaatttacatatgagctttgatcttggtactaaatatggctttgccggtgaacgtttcagGGAGAGAAAGACGACAAAATCATAGCCGTATGTGCTGATGATCCAGAGTACAAACATTTCACAGACATCAAACAACTCGCTCCTCATCGTCTCCAAGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G46860.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 6
gtttgcatagatctttcttagagatcatctaaaagtgcaagctctagaaattgatattgcataagaatcatcaaacttgcaatccaagaaatccaaaatttacatatgagctttgatcttggtactaaatatggctttgccggt--gaacgtttcagGGAGAGAAAGACGACAAAATCATAGCCGTATGTGCTGATGATCCAGAGTACAAACATTTCACAGACATCAAACAACTCGCTCCTCATCGTCTCCAAGAAA
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----------------------------------------------------------gtattgaattcattgatttcttagtcaataaaaccaaccaat--cattcccacattaacaaataaaattaatgtggtattgacatttgaaataatacagGGAGAGAAAGATGATAAAATCATTGCAGTGTGTGCTGATGACCCAGAATATAAACACTTTACAGACTATAGAGAACTTGCACCTCATCGCATCTCTGAGA
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 5
gtttgcatagatctttcttagagatcatctaaaagtgcaagctctagaaattgatattgcataagaatcatcaaacttgcaatccaagaaatccaaaatttacatatgagctttgatcttggtactaaatatggctttgccggtgaacgt--ttcagGGAGAGAAAGACGACAAAATCATAGCCGTATGTGCTGATGATCCAGAGTACAAACATTTCACAGACATCAAACAACTCGCTCCTCATCGTCTCCAAGAAA
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-----------------------------------------------------gtactgaatta-atttattgctttcttagccaatgaaaccaaccatttccacaataaca--aatacaaatat--aatgtggtattgacatttggctcaacacagGGAGAGAAAGATGATAAAATCATTGCAGTGTGTGCTGATGACCCAGAATATAAGCACTTTACTGACTATAGAGAACTTGCACCTCATCGCATCTCCGAGA
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 4
gtttgcatagatctttcttagagatcatctaaaagtgcaagctctagaaattgatattgcataagaatcatcaaacttgcaatccaagaaatccaaaatttacatatgagctttgatcttggtactaaatatggc-tttgccggtgaacgtttcagGGAGAGAAAGACGACAAAATCATAGCCGTATGTGCTGATGATCCAGAGTACAAACATTTCACAGACATCAAACAACTCGCTCCTCATCGTCTCCAAGAAA
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---------------------------------------------------------------------------------------gtagcaaagtgtttacattc---ttttcagcgtttctctaagagtgtcatctatc--tga-----tcagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCAGAGA
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 5
gtttgcatagatctttcttagagatcatctaaaagtgcaagctctagaaattgatattgcataagaatcatcaaacttgcaatccaagaaatccaaaatttacatatgagctttgatcttggtactaaatatggc-tttgccggtgaacgtttcagGGAGAGAAAGACGACAAAATCATAGCCGTATGTGCTGATGATCCAGAGTACAAACATTTCACAGACATCAAACAACTCGCTCCTCATCGTCTCCAAGAAA
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---------------------------------------------------------------------------------------gtagcaaaatgtttacatcc---ttttcagcgtttttctaagagtgtcatctatc--tga-----tcagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCGGAGAMapped 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|19878118|gb|AU238949.1|AU238949EST: GATGTTTNCTCCGTGCTAGAGCCATTGGATTAATGCCCATGATTGATCAG GGAGAGAAAGACGACAAAANCATA
genomic: GATGTTTCCTCCGTGCTAGAGCCATTGGATTAATGCCCATGATTGATCAGgtttgcatag ... aacgtttcagGGAGAGAAAGACGACAAAATCATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatatgagctttgatcttggtactaaatatggctttgccggtgaacgtttcagGGAGAGAAAGACGACAAAATCATAGCCGTATGTGCTGATGATCCAGAGTACAAACATTTCACAGACATCAAACAACTCGCTCCTCATCGTCTCCAAGAAA
tactaaa putative branch site (score: 1)
tactaaatat 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 |
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gtttgcatagatctttcttagagatcatctaaaagtgcaagctctagaaattgatattgcataagaatcatcaaacttgcaatccaagaaatccaaaatttacatatgagctttgatcttggtactaaatatggctttgccggtgaacgtttcagGGAGAGAAAGACGACAAAATCATAGCCGTATGTGCTGATGATCCAGAGTACAAACATTTCACAGACATCAAACAACTCGCTCCTCATCGTCTCCAAGAAA
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