Sequence
atgc intronic sequence ATGC exonic sequenceTTTCAACAAAGTCGGAAAACTCTCGGCAGAGCAGAGAAAAGAGAAGATTCATAGGTATATGAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAAATCAAGgtctttgtgcttaaccatcataaccggattaaaccagtggttatccatataccgatttgttcacatgttttttttgttatattttgttgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04500.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os10g32900.2 (Oryza sativa), 5'ss of exon 3
TTTCAACAAAGTCGGAAAACTCTCGGCAGAGCAGAGAAAAGAGAAGATTCATAGGTATATGAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAAATCAAGgtctt-tgtgcttaaccatcataaccggattaaaccagtggttatccatataccgatttgttcacatgttttttttgttatattttgttgtag-------------------------------------------------
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-----TCAAGACCGTCCGCCTCTCCAACGAGGAGAGGAAGGAAAAGATCCACAGGTACATCAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAGATCAAGGTGAGgcaagaacttccaaattattcaaattcaaattcaaaatatcacccccccccccaacccatatttcaaacgaatttcacctcaccgccgaccacgttactgacatctcagattttttttttaaaaaaaaaatctgcag
upper sequence: AT1G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os10g32900.1 (Oryza sativa), 5'ss of exon 3
TTTCAACAAAGTCGGAAAACTCTCGGCAGAGCAGAGAAAAGAGAAGATTCATAGGTATATGAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAAATCAAGgtctt-tgtgcttaaccatcataaccggattaaaccagtggttatccatataccgatttgttcacatgttttttttgttatattttgttgtag-------------------------------------------------
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GAGCTTCAAGACCGTCCGCCTCTCCAACGAGGAGAGGAAGGAAAAGATCCACAGGTACATCAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAGATCAAGgtgaggcaagaacttccaaattattcaaattcaaattcaaaatatcacccccccccccaacccatatttcaaacgaatttcacctcaccgccgaccacgttactgacatctcagattttttttttaaaaaaaaaatctgcag
upper sequence: AT1G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G21380.1 (Glycine max), 5'ss of exon 4
TTTCAACAAAGTCGGAAAACTCTCGGCAGAGCAGAGAAAAGAGAAGATTCATAGGTATATGAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAAATCAAGgtctttgtgcttaaccatcataaccggattaaaccagtggttatccatataccgatttgttcacatgttttttttgttatatttt----gttgtag--------
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TACCTTGAAGGTTGGAAAACTCTCTGTTGAGCAGAGGAAGGAAAAGATTCATAGATACATGAAGAAGAGAAACGAAAGAAATTTCAGCAAGAAAATCAAGgtact-acatctgaacaccaacattaa--caaacaaatttcaaatcttatactgttttacatg-atttccaatctactgcatcaaccaagccttatgcatattt
upper sequence: AT1G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G26990.1 (Glycine max), 5'ss of exon 2
TTTCAACAAAGTCGGAAAACTCTCGGCAGAGCAGAGAAAAGAGAAGATTCATAGGTATATGAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAAATCAAGgtc-----tttgtgcttaaccatca-taaccggatt--aaaccagtggttatccatataccgatttgttcacatgttttttttgttatattttgt-tgtag------------------------------------------------
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TAACTTGAAAGTTGGAAAACTCTCTGTTGAGCAGAGGAAGGAAAAGATTCATAGATACATGAAGAAGAGAAATGAAAGAAATTTCAGCAAGAAAATCAAGgtactacatctgaacaccaacattaacaaacaaatttgaaatcttatattatgt-tatacatgatttccaatctattgcatcaatcaagccttgtgcatattttcaaaattcaactaatgatccaatgttttttaaaaaaaaaatgcag
upper sequence: AT1G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv05s0049g01830.t01 (Vitis vinifera), 5'ss of exon 3
TTTCAACAAAGTCGGAAAACTCTCGGCAGAGCAGAGAAAAGAGAAGATTCATAGGTATATGAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAAATCAAGgtc------------tttgtgctta-accatcataaccggattaaacca---gtggttatccatataccgatttgttcacatgttttttttgttatattttgttgtag-------------------
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CACTTTCAAGGTTGGAAAACTCTCTGTGGAGCAAAGGAAAGAGAAGATCCATAGATACATGAAGAAAAGGAACGAGAGGAATTTCAGCAAGAAAATCAAGgttatctctctctctctcgttcttctgctatcattttacattcagatcatgtataggcatacgtatgataacttaa--actttattttcttactaaatgttagaaaaatataataataataatgcagMapped 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|19878209|gb|AU239040.1|AU239040EST: ATAGGTATATGAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAAATCAAG TATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGA
genomic: ATAGGTATATGAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAAATCAAGgtctttgtgc ... tttgttgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTCAACAAAGTCGGAAAACTCTCGGCAGAGCAGAGAAAAGAGAAGATTCATAGGTATATGAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAAATCAAGgtctttgtgcttaaccatcataaccggattaaaccagtggttatccatataccgatttgttcacatgttttttttgttatattttgttgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA