Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgattgcttcttttcaggtgtttgaattatgatctaaaactctctgtatcagtatgtttaagtccggatttcttttcttttcacacgttctgttgcagCAGAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAAGAAATTCCAGATGGTTTAAAGCTTCCAGAGTCTTTTAGTCAACTGGTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01040.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G05950.1 (Glycine max), 3'ss of exon 2
gtgagtgattgct---tcttttcaggtgtttg---aattatg----atctaaaactctctgtatcagtatgtttaagtccggatttcttttcttttcacacgttctgttgcagCAGAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAAGAAATTCCAGATGGTTTAAAGCTTCCAGAGTCTTTTAGTCAACTGGTTT
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gtaaataatttttatgttacttcaaatagatatctgattacgtcatatctactcaagttttgattaattaactattatctgaacctttctcgtgatgat-tgtgatgttgcagCAGAGACTAGTTAGAGATCTTTACAATATTCTTAACGAAGTAAAGACTGGGGAAATTCCATCTGCTCTAGAGCTGCCAGATTCATTTGATCAACTGGTTT
upper sequence: AT3G01040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G03460.1 (Glycine max), 3'ss of exon 2
gtgagtgattgcttcttttc-------aggtgtttgaattatg----atctaaaactctctgtatcagtatgtttaagtccggatttcttttcttttcacacgttctgttgcagCAGAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAAGAAATTCCAGATGGTTTAAAGCTTCCAGAGTCTTTTAGTCAACTGGTTT
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gtaaataatttttttgttacttcaaatagatatctga-ttatgtcatatctactaaagatttgattaattaactattatctgaacctttcttgtgatgat-tgtaatgttgcagCAGAGACTAGTTAGAGATTTTTACAATATCCTTAACGAAGTAAAGACTAGGGAAATTCCATCTGCTCTAGAGCTTCCGGATTCATTTGATCAACTGGTTT
upper sequence: AT3G01040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0108g01520.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------gtgagtg--attgcttcttttcaggtgtttgaattatgatctaaaactctctgtatcagta----tgtttaagtccggatttcttttcttttcacacgttc----tgttgcagCAGAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAAGAAATTCCAGATGGTTTAAAGCTTCCAGAGTCTTTTAGTCAACTGGTTT
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gtaaattttgtctttttcttatcctgtagatgttatttttagattgataatgcccgtttgattagttttttttttctttggtggaaatattatttgtgttgttatttaagccaattcctcatggtgatggtgctgcagCAGAGGCTAGTTAGAGATTTTTACAAGATCCTCAATCAAGTGAACACTGAGGAACTCCCAGATGGTCTAAAGCTTCCAGATACATTCAGTCAACTTGTTTMapped 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|116476602|gb|EG519194.1|EG519194EST: TCGGGAGGCGGCTAGGACCACGTCTTCTTGGTAGGATAGATGATTCAGAG CAGAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAA
genomic: TCGGGAGGCGGCTAGGACCACGTCTTCTTGGTAGGATAGATGATTCAGAGgtgagtgatt ... tctgttgcagCAGAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAA
EST:
gi|116476805|gb|EG519397.1|EG519397EST: GGAGGAGGCTAGGACCACGTCTTCTTGGTAGGATAGATGATTC--AG -AGAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAA
genomic: GGAGGCGGCTAGGACCACGTCTTCTTGGTAGGATAGATGATTCAGAGgtgagtgatt ... tctgttgcagCAGAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtatcagtatgtttaagtccggatttcttttcttttcacacgttctgttgcagCAGAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAAGAAATTCCAGATGGTTTAAAGCTTCCAGAGTCTTTTAGTCAACTGGTTT
tttcttttcttttcac CT-rich tract
atttcttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgattgcttcttttcaggtgtttgaattatgatctaaaactctctgtatcagtatgtttaagtccggatttcttttcttttcacacgttctgttgcagCAGAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAAGAAATTCCAGATGGTTTAAAGCTTCCAGAGTCTTTTAGTCAACTGGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG