Sequence
atgc intronic sequence ATGC exonic sequencegtttgtttttgaacttaagcttagaaatgtatgtttgatattctgtttggtaattttgttttcttacttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53090.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53090.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G461948_T01 (Zea mays), 3'ss of exon 12
gtttgtttttgaacttaagcttagaaatgtatgtttgatattc----tgtttggtaattttgttttcttac------ttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG
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-tccgttcttggtttttc-tacagtgatatcaacttgagactcataatgtgctctaaatttgtttatgcaagaacgataattaacgttgttacttgatgtagGTTCCATGTGATGTAACACTTTGGGCATCAATTGGAGGCCAAGATGTAGATCGTCTTCCATCTGCTTCCACATGCTACAATACGCTCAAG
upper sequence: AT3G53090.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA03G34650.1 (Glycine max), 3'ss of exon 13
------gtttgtttttgaacttaagcttagaaatgtatgtttgatattct---gtttggtaattttgttttcttacttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG
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tttgcaacatcatgatccagtcatgtgttgaaagaatccctaaaaataataaaatgtattgattccattgattaacattcatgtctatttgtttac-acagGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGATCGACTTCCATCAGCTTCAACCTGCTACAATACTCTTAAG
upper sequence: AT3G53090.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA19G37310.2 (Glycine max), 3'ss of exon 14
-------gtttgtttttgaacttaagcttagaaatgtatgtt----tgatattctgtttggtaattttgttttcttacttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG
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tttgcaacatcatgatccagttatgggttggaagaatccctaaaaataataaaatgtct--tgattccattgattggcattcatgtctatttgtttacaa-agGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGATCGGCTTCCATCAGCTTCAACCTGCTACAATACCCTTAAGMapped 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|47830785|gb|CK120469.1|CK120469EST: CACCACTCCTTGGTTTCAAATACTTGCAGCCAACCTTCATCATCCATAAA GTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAA
genomic: CACCACTCCTTGGTTTCAAATACTTGCAGCCAACCTTCATCATCCATAAAgtttgttttt ... tcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattctgtttggtaattttgttttcttacttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG
ttcttac putative branch site (score: 2)
ttttgttttcttactt CT-rich tract
taattttgttttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtttttgaacttaagcttagaaatgtatgtttgatattctgtttggtaattttgttttcttacttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG