Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaacgtctgaaatctttcttacgtatttcaacaaaaagaagttcaaagttttgattttgttctcttggtttgtatgttttgcttaaaagGTTTTAGAGATCCGTCCTGTGATTGACTGGGACAAAGGGAAAGCTGTGACATTTCTACTTGAATCACTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51460.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51460.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G36570.1 (Glycine max), 3'ss of exon 8
------------gtaaaaacgtctgaaatctttcttacgtatttcaacaaaaagaagttcaaagttttgattttgttctct-tggtttgtatgttttgcttaaaagGTTTTAGAGATCCGTCCTGTGATTGACTGGGACAAAGGGAAAGCTGTGACATTTCTACTTGAATCACTCG
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gtactgtttttagtgccaaagccaaccttttgactcattttttaggagattcaactgttcaatgcttaaaatttctcgtttataatttctgcttactattttta-gGTTTTAGAGATCCGACCTGTGATTAACTGGGATAAGGGCAAAGCTGTCACGTTTCTACTTGAGTCACTTG
upper sequence: AT5G51460.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G00790.1 (Glycine max), 3'ss of exon 8
---------gtaaaaacgtctgaaatct-ttcttacgtatttcaacaaaaagaa--gttcaaagttttgattttgttctcttggtttgtatgttttgcttaaaagGTTTTAGAGATCCGTCCTGTGATTGACTGGGACAAAGGGAAAGCTGTGACATTTCTACTTGAATCACTCG
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gtactgtttttagagccaaagccaacctgttgagtcattttttaggagattcaactgttcaatgcttagatttctcgtttataatttttgcttactatttttcagGTTTTAGAGATCCGACCTGTGATTAACTGGGATAAGGGAAAAGCTGTCACGTTTTTACTTGAGTCACTTG
upper sequence: AT5G51460.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G47630.2 (Glycine max), 3'ss of exon 7
gtaaaaacgtctgaaatctttcttacgtatttcaacaaaaagaagttcaaagttttgattttgttctcttggtttgtatgttttgcttaaaagGTTTTAGAGATCCGTCCTGTGATTGACTGGGACAAAGGGAAAGCTGTGACATTTCTACTTGAATCACTCG
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gtactatt-tctagacccaaatttatcactcgttttttaaaaagatctaactgttaaagtactttttaataatctatgtttactaattttcagGTTTTAGAGGTTCGGCCAGTGATTGACTGGGATAAGGGAAAAGCTGTCACATTTCTACTTGAGTCACTTG
upper sequence: AT5G51460.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G13880.1 (Glycine max), 3'ss of exon 8
---gtaaaaacgtctgaaatctttcttacgtatttcaacaaaaagaagt-tcaaagttttgattttgttctcttggtttgtatgttttgcttaaaagGTTTTAGAGATCCGTCCTGTGATTGACTGGGACAAAGGGAAAGCTGTGACATTTCTACTTGAATCACTCG
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gtagtttctagaccaaaaattttcactcattttttcaagagatctaactgttaaagt----acttt-ttttaataatccatgtttattaattttcagGTTTTAGAGGTTCGGCCAGTGATTGACTGGGATAAGGGAAAAGCTGTCACATTTTTACTCGAGTCACTTG
upper sequence: AT5G51460.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 7
gtaaaaacgtctgaaatctttct-tacgtatttcaacaaaaagaagttcaaagttttgattttgttctcttggtttgtatgttttgcttaaaagGTTTTAGAGATCCGTCCTGTGATTGACTGGGACAAAGGGAAAGCTGTGACATTTCTACTTGAATCACTCG
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---gtaatctttggaatgatgttgtagatttttcaatatatta---tcttcagcttgtccttttcttttctgaaccccacttattaatgattagGTTTTAGAGGTCCGACCTGTGATTGACTGGGATAAGGGAAAAGCTGTTGAGTTTTTACTTGAGTCACTTGMapped 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|47828165|gb|CK117849.1|CK117849EST: ATGATGTCATCAGAACATATCCAAAACTACGGCTAACACATGGCCGGAAG GTGTTAGAGATCCGTCCTGTGATTGACTGGGACAAAGGGAAAGCTGTGACA
genomic: ATGATGTCATCAGAACATATCCAAAACTACGGCTAACACATGGCCGGAAGgtaaaaacgt ... tgcttaaaagGTTTTAGAGATCCGTCCTGTGATTGACTGGGACAAAGGGAAAGCTGTGACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagaagttcaaagttttgattttgttctcttggtttgtatgttttgcttaaaagGTTTTAGAGATCCGTCCTGTGATTGACTGGGACAAAGGGAAAGCTGTGACATTTCTACTTGAATCACTCG
ttttgat putative branch site (score: 4)
ttttgctt putative PPT
aaagttttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaacgtctgaaatctttcttacgtatttcaacaaaaagaagttcaaagttttgattttgttctcttggtttgtatgttttgcttaaaagGTTTTAGAGATCCGTCCTGTGATTGACTGGGACAAAGGGAAAGCTGTGACATTTCTACTTGAATCACTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG