Sequence
atgc intronic sequence ATGC exonic sequencegtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctagGTTGGCCTGCTTTTCACCAGTCAAATGTGCACTCGAGTCCTCTTCTATTTGATATCGACAAAGATGGTGTTAGAGAAATTGCTCTGGCTACCTACAATGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G09090.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g61050.1 (Oryza sativa), 3'ss of exon 3
gtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctagGTTGGCCTGCTTTTCACCAGTCAAATGTGCACTCGAGTCCTCTTCTATTTGATATCGACAAAGATGGTGTTAGAGAAATTGCTCTGGCTACCTACAATGC
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-------------------ccacattttaaaggtcctgaaagtttgtgctataattaa--caaaagaattggtttaatgttgtttatttattaatatatattgttgtgaaattga--ttccagGATGGCCTGCATTTCACCAGTCAAATGTTCATTCAAGTCCACTTCTATATGATATTGACAAGGACGGGACACGGGAAATAGTTTTGGCAACTTACAATGG
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G14690.1 (Glycine max), 3'ss of exon 3
gtacaagatatcttatcttctttacctttagctttctgaaattttatt-ttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctagGTTGGCCTGCTTTTCACCAGTCAAATGTGCACTCGAGTCCTCTTCTATTTGATATCGACAAAGATGGTGTTAGAGAAATTGCTCTGGCTACCTACAATGC
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-------------------gttaatgcttaggatcgaagcttgtccttattgtgattgattgattaacttaggtttgattttgagttttataaaaca-----taatcttctgaatggttctcagGCTGGCCTGCTTTCCACCAATCAACTGTGCATTCTAGTCCTCTTCTATATGACATTGACAAAGATGGAGTGAGAGAAATAGCTTTGGCAACCTACAATGG
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G27250.1 (Glycine max), 3'ss of exon 3
gtacaagatatcttatcttctttacctttagctttctgaaattttatt-ttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctagGTTGGCCTGCTTTTCACCAGTCAAATGTGCACTCGAGTCCTCTTCTATTTGATATCGACAAAGATGGTGTTAGAGAAATTGCTCTGGCTACCTACAATGC
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-------------------gttaatgcttaggatcaagacttgtcctagttgtgattgattgattaacttgggtttgaatttgagttttataaaaaa-----taatcttctgaatggttcttagGCTGGCCAGCATTCCACCAATCAACTGTGCATTCTAGTCCTCTTCTATATGACATTGACAAAGATGGAGTGAGAGAAATAGCTTTGGCAACCTACAATGG
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g01790.t01 (Vitis vinifera), 3'ss of exon 3
gtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatt-tgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctagGTTGGCCTGCTTTTCACCAGTCAAATGTGCACTCGAGTCCTCTTCTATTTGATATCGACAAAGATGGTGTTAGAGAAATTGCTCTGGCTACCTACAATGC
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-----------------------atattttattgatgaaagaaaagtgctacttatggagaaatgcaatgatactgattttcccagatgcttgtattgagtttaatgctgttatacatatc-agGCTGGCCTGCATTTCACCAGTCAACTGTCCATTCCAGTCCTCTTCTGTATGATATCGACAAGGATGGTGTAAGAGAAATAGCTTTGGCTACCTACAATGGMapped 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|152035986|gb|AU236941.2|AU236941EST: TGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG GTTGGCCTGCTTTTCACCAGTCAAATGTGCACTCGAGTCCTCTTCTATTTG
genomic: TGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAGgtacaagata ... aaatttctagGTTGGCCTGCTTTTCACCAGTCAAATGTGCACTCGAGTCCTCTTCTATTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctagGTTGGCCTGCTTTTCACCAGTCAAATGTGCACTCGAGTCCTCTTCTATTTGATATCGACAAAGATGGTGTTAGAGAAATTGCTCTGGCTACCTACAATGC
tactgat putative branch site (score: 2)
tttct putative PPT
aatattaaggatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctagGTTGGCCTGCTTTTCACCAGTCAAATGTGCACTCGAGTCCTCTTCTATTTGATATCGACAAAGATGGTGTTAGAGAAATTGCTCTGGCTACCTACAATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG