Sequence
atgc intronic sequence ATGC exonic sequenceGTGTTCAGATATGGGTGTCGAGGATTATCATGTGATAGAGCTTGTCGGTGAAGGATCTTTTGGGAGGGTTTACAAAGGAAGACGCAAGTATACCGGCCAGgtaaattgttgctgggttgttctctttgttatcatcggctacttaaaatcagctaatcaattcttaatttggtaatttttatcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G50240.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G50240.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv16s0039g02400.t01 (Vitis vinifera), 5'ss of exon 1
GTGTTCAGATATGGGTGTCGAGGATTATCATGTGATAGAGCTTGTCGGTGAAGGATCTTTTGGGAGGGTTTACAAAGGAAGACGCAAGTATACCGGCCAGgtaaattgttgctgggttgttctctt-tgttatcatcggct---acttaaaatcagctaatcaattcttaatttggta--atttttatcag------
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--------AGATGGGTGTCGAAAATTATCATGTAATTGAGCTGGTAGGTGAAGGTTCTTTTGGGAAGGTATACAAAGGAAGGCGGAAGTTTACAGGGCAGgtac-ttgttgcaattcccttctcttgccttttgagtgaattggaggtggtttgacttgcttcatccttatcttagtgctgttttaattgatctcag
upper sequence: AT1G50240.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ33693 (Selaginella moellendorffii), 5'ss of exon 1
GTGTTCAGATATGGGTGTCGAGGATTATCATGTGATAGAGCTTGTCGGTGAAGGATCTTTTGGGAGGGTTTACAAAGGAAGACGCAAGTATACCGGCCAGgtaaattgttgctgggttgttctctttgttatcatcggctacttaaaatcagctaatcaattcttaatttggtaatttttatcag
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----------ATGGGCGTCGAGAACTATCATGTGATCGAGCTCGTCGGCGAGGGATCGTTTGGGAAGGTCTACAAGGGAAGGCGCAAGTTCACTGGCCAGgt------tctgtgagcta--cattttgtttttcttgcttgcccctgatcgatcgatcgaccag---------------------
upper sequence: AT1G50240.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ37043 (Selaginella moellendorffii), 5'ss of exon 1
GTGTTCAGATATGGGTGTCGAGGATTATCATGTGATAGAGCTTGTCGGTGAAGGATCTTTTGGGAGGGTTTACAAAGGAAGACGCAAGTATACCGGCCAGgtaaattgttgctgggttgttctctttgttatcatcggctacttaaaatcagctaatcaattcttaatttggtaatttttatcag
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----------------GTCGAGAACTATCATGTGATCGAGCTCGTCGGCGAGGGATCGTTCGGGAAGGTCTACAAGGGAAGGCGCAAGTTCACTGGCCAGGTTCATt----ttggttttcttgcttgcccctgatcgatcgatcgac--------------------------------------Mapped 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|164045354|gb|ES201347.1|ES201347EST: AAGGATCTTTTGGGAGGGTTTACAAAGGAAGACGCAAGTATACCGGCCAG ACGGTGGCGATGAAGTTCATCATGAAACAAGGAAAGACTGACAAGGATATA
genomic: AAGGATCTTTTGGGAGGGTTTACAAAGGAAGACGCAAGTATACCGGCCAGgtaaattgtt ... tttttatcagACGGTGGCGATGAAGTTCATCATGAAACAAGGAAAGACTGACAAGGATATA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGTTCAGATATGGGTGTCGAGGATTATCATGTGATAGAGCTTGTCGGTGAAGGATCTTTTGGGAGGGTTTACAAAGGAAGACGCAAGTATACCGGCCAGgtaaattgttgctgggttgttctctttgttatcatcggctacttaaaatcagctaatcaattcttaatttggtaatttttatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA