Sequence
atgc intronic sequence ATGC exonic sequencegtaatgataccctttttacaaacaattcgtctttactgatttgtataatctctgagcaatcataaccttttattttattggggacttgattgttaaatctcagGGAAAAGTTGAAGTGACAATAGCAGGAGGACGAATTGTGTGGGAAAACGAGGAACTTAAAGTTGTTCCAAGAAGTGGCAAGTATATAGAGATGCCTCCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G12200.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA14G04030.2 (Glycine max), 3'ss of exon 8
gtaatgataccctttttacaaacaattcgtctttactgatttgtataatctctgagcaatcataaccttttattttattggggacttgattgttaaatctcagGGAAAAGTTGAAGTGACAATAGCAGGAGGACGAATTGTGTGGGAAAACGAGGAACTTAAAGTTGTTCCAAGAAGTGGCAAGTATATAGAGATGCCTCCTT------------------------------------------------------------
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----------------------------------------------------------gtcattcaatatcaagat-tcaaagtttttattttt----ctcagggaaaaattgaagtgactattgcaggaggaagagttgtttgggaaaataatgaactaaagGTCACTCCTGGCACTGGGAGATACATCCAAATGCCACCTTTTAGTTATCTGTTTGATGGACTGGACAAAAAGGACGCCATTTATCTAAATTCCCTTCAGG
upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA14G04030.1 (Glycine max), 3'ss of exon 12
gtaatgataccctttttacaaacaattcgtc-tttactgatttgtataatctctgagcaatcataaccttttattttat-tggggacttga--ttgttaaat--ctcagGGAAAAGTTGAAGTGACAATAGCAGGAGGACGAATTGTGTGGGAAAACGAGGAACTTAAAGTTGTTCCAAGAAGTGGCAAGTATATAGAGATGCCTCCTT
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---gtaccggtttaactataatctgttcattatatgattgtttgtgtattgttcaacaattgaaggcttgtcattcaatatcaagattcaaagtttttatttttctcagGGAAAAATTGAAGTGACTATTGCAGGAGGAAGAGTTGTTTGGGAAAATAATGAACTAAAGGTCACTCCTGGCACTGGGAGATACATCCAAATGCCACCTT
upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 12
gtaatgataccctttttacaaacaattcgtctttactgatttgtataatctctgagcaatcataac-cttttattttattgg--ggacttgattgttaaa----tctcagGGAAAAGTTGAAGTGACAATAGCAGGAGGACGAATTGTGTGGGAAAACGAGGAACTTAAAGTTGTTCCAAGAAGTGGCAAGTATATAGAGATGCCTCCTT
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---gttatattctttct-----cattatgtttgta-tgtataagataaacattga-tattcatattgcatatatattagggtttgaaaaagaatgttatgattttctcagGGAAAGGTTGAGGTGACAATTGCTGGAGGAAAAATTGTTTGGGAAAATGATGAACTGAAGGCAGTTCCTGGATCTGGAAAGTACATAGAAATGCAACCTTMapped 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|125152778|gb|EL184250.1|EL184250EST: CTCATCATTCAAGATCAGACACAAACGTCTACGAGGGCAGAAGAGG-AAG GGAAAAGTTGAAGTGACAATAGCAGGAGGACGAATTGTGTGGGAAAACGAG
genomic: CTCATCATTCAAGATCAGACACAAACGTCTACGAGGGCAGAAGAGGAAAGgtaatgatac ... taaatctcagGGAAAAGTTGAAGTGACAATAGCAGGAGGACGAATTGTGTGGGAAAACGAG
EST:
gi|124828016|gb|EH912882.1|EH912882EST: TCATCATTCAAGATCAGACACAAACGTCTAACGAGGGCAGAAGAGGAAAG GGAAAAGTTGAAGTGA
genomic: TCATCATTCAAGATCAGACACAAACGTCTA-CGAGGGCAGAAGAGGAAAGgtaatgatac ... taaatctcagGGAAAAGTTGAAGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctgagcaatcataaccttttattttattggggacttgattgttaaatctcagGGAAAAGTTGAAGTGACAATAGCAGGAGGACGAATTGTGTGGGAAAACGAGGAACTTAAAGTTGTTCCAAGAAGTGGCAAGTATATAGAGATGCCTCCTT
aatcataaccttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgataccctttttacaaacaattcgtctttactgatttgtataatctctgagcaatcataaccttttattttattggggacttgattgttaaatctcagGGAAAAGTTGAAGTGACAATAGCAGGAGGACGAATTGTGTGGGAAAACGAGGAACTTAAAGTTGTTCCAAGAAGTGGCAAGTATATAGAGATGCCTCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG