Sequence
atgc intronic sequence ATGC exonic sequencegtttcattttttctattcttttcacattttttttcctgtaaaaatctcatcttttctgcaatttggtttgaatcatgaatcaattcatatcttggagattttttatgggaaatggaaaactttttcattgctctaagttaactttagctggattctgcttatgtgtaattgaatcagGTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATCATGGACAAAAAGTTTATCACCAAGGAGAATAAAACAGCTTATGTCAAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G10540.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g65230.1 (Oryza sativa), 3'ss of exon 1
gtttcattttttctattcttttcacattttttttcctgtaaaaatctcatcttttctgcaatttggtttgaatcatgaatcaattcatatcttggagattttttatgggaaatggaaaactttttcattgctctaagttaactttagctggattctgcttatgtgtaattgaatcagGTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATCATGGACAAAAAGTTTATCACCAAGGAGAATAAAACAGCTTATGTCAAAT
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---------------------------------------------------------gtgttttgatttgatt----gatcggttcgcatgc-gatgatgccccctgatcatccg----cgttctcgtggttct----tgtgcctggtggtgtcattcatg-gtggaatttgg-cagGTGGTGAGGGCCAAGAAGAAGGATACGGGGAATGTGTACGCGCTCAAGATCATGGACAAGAAGTTCATCACCAAGGAGAACAAGATCTCCTACGTCAAGA
upper sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G097821_T02 (Zea mays), 3'ss of exon 1
gtttcattttttctattcttttcacattttttttcctgtaaaaatctcatcttttctgcaatttggtttgaatcatgaatcaattcatatcttggagattttttatgggaaatggaaaactttttcattgctctaagttaactttagctggattctgcttatgtgtaattgaatcagGTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATCATGGACAAAAAGTTTATCACCAAGGAGAATAAAACAGCTTATGTCAAAT
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------------------------------------------------------------gttctctt---actgctactcactgcatgggtgtgccatggcctgcgcggccgcgtggatcgtgggacgattt---attcaccgaggcgggacgatga--aaaaaaaaatga--cagGTGGTGCGGGCCAAGAAGAAGGACACTGGTCGCGTCTACGCGCTTAAGATCATGGACAAGAAGTTCATCACCAAGGAGAACAAGATCTCCTACGTCAAGA
upper sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 1
gtttcattttttctattcttttcacattttttttcctgtaaaaatctcatcttttctgcaatttggtttgaatcatgaatcaattcatatcttggagattttttatgggaaatggaaaactttttcattgctctaagttaactttagctggattctgcttatgtgtaattgaatcagGTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATCATGGACAAAAAGTTTATCACCAAGGAGAATAAAACAGCTTATGTCAAAT
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-------------------------------------------------------------------tggaacttttttttttgctattatgtggtgaacagttgtttga----gtgtatttattttctcttgtaaatcatcaccaaat--atcttacttat-tatgtttaaa---gGTTGTGAGGGCAAAGAAGAAGGACACTGGAACTGTGTATGCATTGAAGATCATGGACAAAAAATTTATTACCAAAGAGAATAAAACAGCTTATGTGAAGT
upper sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G34430.1 (Glycine max), 3'ss of exon 1
gtttcattttttctattcttttcacattttttttcctgtaaaaatctcatcttttctgcaatttggtttgaatcatgaatcaattcatatcttggagattttttatgggaaatggaaaactttttcattgctctaagttaactttagctggatt-ctgcttatgtgtaattgaatcagGTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATCATGGACAAAAAGTTTATCACCAAGGAGAATAAAACAGCTTATGTCAAAT
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----------------------------------------------------------------acttttttttcccctctgttatatatgctgaacagttgttt----gagtgga---tttatctactcttgtaaattatcaccaaatatctttcttcttatgtttaa-------agGTTGTGAGGGCAAAGAAGAAGGACACTGGAATTGTGTACGCATTGAAGATCATGGACAAAAAATTTATTACCAAAGAGAACAAAACAGCTTATGTGAAGT
upper sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0074g00100.t01 (Vitis vinifera), 3'ss of exon 2
gtttcattttttctattcttttcacattttttttcctgtaaaaatctcatcttttctgcaatttggtttgaatcatgaatcaattcatatcttgga--gattttttatgggaaatggaaaactttttcattgctctaagttaactttagctggattctgcttatgtgtaattgaatc-agGTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATCATGGACAAAAAGTTTATCACCAAGGAGAATAAAACAGCTTATGTCAAAT
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---------------------------------------------------------------------------tgggcacttacgcatctggaattgatgtctggttttaattgttagcatttgggtatgtggttatttatttgtttctttatt----ttatat-caattgactccagGTTGTGAGGGCAAGGAAGAAGGACACTGGAATTGTGTACGCTTTGAAAATCATGGACAAAAAGTTCATCACAAAAGAAAATAAAACAGCTTATGTGAAGTMapped 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|86070402|gb|DR366159.1|DR366159EST: ACCATGATTTCGAGCTCGGCAAGATCTATGGCGTTGGCTCTTATTCTAAG GTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATC
genomic: ACCATGATTTCGAGCTCGGCAAGATCTATGGCGTTGGCTCTTATTCTAAGgtttcatttt ... attgaatcagGTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATC
EST:
gi|86070404|gb|DR366161.1|DR366161EST: ACCATGATTTCGAGCTCGGCAAGATCTATGGCGTTGGCTCTTATTCTAAG GTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATC
genomic: ACCATGATTTCGAGCTCGGCAAGATCTATGGCGTTGGCTCTTATTCTAAGgtttcatttt ... attgaatcagGTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcattgctctaagttaactttagctggattctgcttatgtgtaattgaatcagGTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATCATGGACAAAAAGTTTATCACCAAGGAGAATAAAACAGCTTATGTCAAAT
agttaac putative branch site (score: 3)
ttaacttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttcattttttctattcttttcacattttttttcctgtaaaaatctcatcttttctgcaatttggtttgaatcatgaatcaattcatatcttggagattttttatgggaaatggaaaactttttcattgctctaagttaactttagctggattctgcttatgtgtaattgaatcagGTTGTTAGGGCGAAGAAGAAGGATAATGGAACTGTGTATGCCTTGAAGATCATGGACAAAAAGTTTATCACCAAGGAGAATAAAACAGCTTATGTCAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA