Sequence
atgc intronic sequence ATGC exonic sequenceTAAAGCTAAGCATTAAGTCCTTTAGGATTCCAGAGCTTTTTATTGAAGTTCCAGAAACTGCAACAGTAGGATCACTAAAGgtatatgccaatatgtatttcttcacatttgtttggttctcttgtgtggacattgaggtgttaacaaattaccattttgctctttgacccttttggttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12560.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12560.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA11G34050.2 (Glycine max), 5'ss of exon 5
TAAAGCTAAGCATTAAGTCCTTTAGGATTCCAGAGCTTTTTATTGAAGTTCCAGAAACTGCAACAGTAGGATCACTAAAGgtata------------tgccaatatgtatttcttcacatttgtttggttctcttgtgtggacattgaggtgttaacaaa----ttaccattttgctct--ttgacccttttggttgcag-----------
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TAAAGTTTAGCATAAAGTCAATAAGGATTCCAGAGCTTTATATTGAGGTTCCTGAAACTTCAACTGTTGGTTCACTAAAGgtataaatagagacaaataaagagatagcttaacttccattttttcaataattcattaccgttgtcaaagcatcattaatgcatttgcagtcttgtcttgctctaacctttgcattatatattctttgtag
upper sequence: AT3G12560.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G04250.1 (Glycine max), 5'ss of exon 4
TAAAGCTAAGCATTAAGTCCTTTAGGATTCCAGAGCTTTTTATTGAAGTTCCAGAAACTGCAACAGTAGGATCACTAAAGgtatatgccaatatgt--atttcttcacatttgtttggttctcttgtgtggaca-ttga--ggtgttaacaaattaccattt-tgctctttgaccct--tttggttgcag-------------------------
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TAAAGTTTAGCATAAAGTCTATAAGGATACCAGAGCTTTATATTGAGGTTCCTGAAACTTCAACTGTTGGTTCACTAAAGgtataaataaagacagcaaaataaagagatagtttcacttctatttttttaataattcattactgttgtcaaagcatcattaatgcatttgcagtcttgtctggctctaacctttgcattgtatattctttgtag
upper sequence: AT3G12560.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv13s0019g01670.t01 (Vitis vinifera), 5'ss of exon 6
TAAAGCTAAGCATTAAGTCCTTTAGGATTCCAGAGCTTTTTATTGAAGTTCCAGAAACTGCAACAGTAGGATCACTAAAGgtatatgccaatatgtatttcttcacatttgtttggttctcttgtgtggacattgaggtgttaacaaattaccattttgctct---ttgacccttttggttgcag
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TGAAGTTTAGCATTAAGTCCTTCAGGGTACCGGAGCTTTTTATTGAGGTTCCTGAAACTGAAACTATTGGTGCATTGAAGgtgtgtaattctgtagatacctcca-acacacacgcacaaaaaaaaaaaaaaaaaggaataaaataaaacactatgatgtttcaaatttagtatctccttt----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|164159486|gb|ES175636.1|ES175636EST: GTTCCAGAAACTGCAACAGTAGGATCACTAAAG AGGACTGTGATGGAGGCTGTCAGTGTTTTACTCAGCGGAGGAATACGTGTT
genomic: GTTCCAGAAACTGCAACAGTAGGATCACTAAAGgtatatgcca ... ttggttgcagAGGACTGTGATGGAGGCTGTCAGTGTTTTACTCAGCGGAGGAATACGTGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TAAAGCTAAGCATTAAGTCCTTTAGGATTCCAGAGCTTTTTATTGAAGTTCCAGAAACTGCAACAGTAGGATCACTAAAGgtatatgccaatatgtatttcttcacatttgtttggttctcttgtgtggacattgaggtgttaacaaattaccattttgctctttgacccttttggttgcag
- - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - TTGAAG