Sequence
atgc intronic sequence ATGC exonic sequenceTTCAGCGAGGTTGTTTGATGCCATTGTCAGTGGCTGTATACCTGTTATAGTCAGTGACGAGTTGGAATTTCCTTTTGAAGGAATACTTGATTACAAGAAGgtatgctagaaaacgtattacattggtgctctgaattataaccattttttgtctgaattagtttagatatgaagcaaagtttgtatgactgttcgctctcttttcttttgcttttgtttacctttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16890.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16890.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g59630.1 (Oryza sativa), 5'ss of exon 6
TTCAGCGAGGTTGTTTGATGCCATTGTCAGTGGCTGTATACCTGTTATAGTCAGTGACGAGTTGGAATTTCCTTTTGAAGGAATACTTGATTACAAGAAGgtatgctagaaaacgtattacattggtgctctgaattataaccattttttgtctgaattagtttagatatgaagcaaagtttgtatgactgttcgctctcttttcttttgcttttgtttacctttcag
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TTCTGCTCGTCTGTTTGATGCAATTGTTAGTGGTTGCATACCAGTTATAGTCAGTGATGAACTAGAGCTTCCTTTTGAAGGAATACTTGACTACAGGAAGgtaaacttgatttatcgcagtattaatgcactgt----------tttctcataccacatatcttag--------taaaggtttta---ctacgtactccctctgtttcaggttataag-acg------
upper sequence: AT5G16890.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G11550.1 (Glycine max), 5'ss of exon 6
TTCAGCGAGGTTGTTTGATGCCATTGTCAGTGGCTGTATACCTGTTATAGTCAGTGACGAGTTGGAATTTCCTTTTGAAGGAATACTTGATTACAAGAAGgtatgctagaaaacgtattacattggtgctctgaattataaccattttttgtctgaattagtttagatatgaagcaaagtttgt-atgactgttcgctctcttttcttttgcttttgtttacctttcag
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CTCTGCTAGATTATTTGATGCTATTGTCAGTGGATGCATTCCAGTTATAATAAGTGATGAGCTGGAGCTTCCTTTCGAAGGAATACTTGATTACAGGAAGgtgtgcttgcatttatatcatgtaactgattacattaagaacaatattgagagttaat-ggtataattgcaataaaatagtggtgaaaataattcactagc----------------------------
upper sequence: AT5G16890.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA12G02010.1 (Glycine max), 5'ss of exon 6
TTCAGCGAGGTTGTTTGATGCCATTGTCAGTGGCTGTATACCTGTTATAGTCAGTGACGAGTTGGAATTTCCTTTTGAAGGAATACTTGATTACAAGAAGgtatgctagaaaacgtattacattggtgctctgaattataaccattttttgtctgaattagtttagatatgaagcaaagtttgtatgactg-ttcgctctcttttcttttgcttttgtttacctttcag
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CTCTGCTAGATTATTTGATGCAATTGTCAGTGGATGCATTCCGGTTATAATAAGTGATGAGCTGGAGCTTCCTTTCGAAGGAATTCTTGATTACAGGAAGgtgtgt--atatttatatcatgtaactgattacattaagaacaacattgagagttaac-ggtataattgcaataaaatagtggtgaaaataactcactagctt--------------------------
upper sequence: AT5G16890.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv19s0014g00560.t01 (Vitis vinifera), 5'ss of exon 6
TTCAGCGAGGTTGTTTGATGCCATTGTCAGTGGCTGTATACCTGTTATAGTCAGTGACGAGTTGGAATTTCCTTTTGAAGGAATACTTGATTACAAGAAGgtatgctagaaaacgtattacattggtgctctgaattataaccattttttgtctgaattagtttagatatgaagcaaagtttgtatgactgttcgctctcttttcttttgcttttgtttacctttcag
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CTCTGCTAGATTGTTTGACGCTATTGTTAGTGGGTGCATCCCTGTTATAGTTAGTGATGAACTGGAGCTTCCTTTTGAAGGAATACTTGATTACCGGAAGgtatgcatgcaatcatg--aagcttgtgttgttatttttggaagtttttaa----aacaaaactcatcactaaaccctgttc-tgcatcaatttaatttgttaatgg---------------------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|86084690|gb|DR380449.1|DR380449EST: TCAGTGACGAGTTGGAATTTCCTTTTGAAGGAATACTTGATTACAAGAAG GTTGCTGTGCTTGTTTCTTCCAGTGATGCAATACAGCCAGGGTGGCTTGTA
genomic: TCAGTGACGAGTTGGAATTTCCTTTTGAAGGAATACTTGATTACAAGAAGgtatgctaga ... tacctttcagGTTGCTGTGCTTGTTTCTTCCAGTGATGCAATACAGCCAGGGTGGCTTGTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTCAGCGAGGTTGTTTGATGCCATTGTCAGTGGCTGTATACCTGTTATAGTCAGTGACGAGTTGGAATTTCCTTTTGAAGGAATACTTGATTACAAGAAGgtatgctagaaaacgtattacattggtgctctgaattataaccattttttgtctgaattagtttagatatgaagcaaagtttgtatgactgttcgctctcttttcttttgcttttgtttacctttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG