Sequence
atgc intronic sequence ATGC exonic sequenceGGTTGCTCCAAAATCAACACTTGGTAATTGGATGAACGAAATTCGCCGGTTTTGTCCTGTCCTACGTGCTGTGAAGTTCCTTGGTAATCCTGAGGAGAGGgtaagtcatgagctgtctgccatttcagaatttcatgtaaacgtttatcccaggattctgaaatgtctgctaactgatgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06400.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 6
GGTTGCTCCAAAATCAACACTTGGTAATTGGATGAACGAAATTCGCCGGTTTTGTCCTGTCCTACGTGCTGTGAAGTTCCTTGGTAATCCTGAGGAGAGGgtaagtc-atgagctgtctgccatttcagaatttcatgtaaacg-tttatcccaggattctgaaatgtctgctaactgatgcag---
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TGTTGCACCAAAGTCTACTCTTGGCAACTGGATAAAGGAAATTCAACGGTTTTGCCCTATTCTACGTGCTGTGAAATTCTTAGGGAATCCAGAAGAGAGGgttagtttacttagcctccgct-ctccaaccattcttatgaacaacttctgatgttgtactgaacattttgcattctgtttggtcag
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 6
GGTTGCTCCAAAATCAACACTTGGTAATTGGATGAACGAAATTCGCCGGTTTTGTCCTGTCCTACGTGCTGTGAAGTTCCTTGGTAATCCTGAGGAGAGGgtaagtcatgagctgtctgcc--atttcagaatttcatgtaaacgtttatcccaggattctgaaatgtctg-ctaactgatgcag----------
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GGTTGCTCCAAAATCTACTCTTGGAAATTGGATGAATGAAATTCGGCGCTTTTGCCCTGTTTTACGTGCTGTAAAGTTCCTTGGCAATCCTGACGAAAGGgtaagactagccttgctgaaccaaattacttgttttaagattacaattaatgcttgcttctgatgcttttgtctaatggtttcaaataacttcag
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G38050.2 (Glycine max), 5'ss of exon 6
GGTTGCTCCAAAATCAACACTTGGTAATTGGATGAACGAAATTCGCCGGTTTTGTCCTGTCCTACGTGCTGTGAAGTTCCTTGGTAATCCTGAGGAGAGGgtaagtcatgagctgtctg---ccatttcagaatttcatgtaaacgtttatcccaggattctgaaatgtctg-ctaactgatgcag----------
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GGTTGCTCCAAAATCTACTCTTGGAAATTGGATGAATGAAATTCGGCGCTTTTGCCCTGTTTTACGCGCTATAAAGTTCCTTGGCAATCCTGACGAAAGGgtaagac-tagcctttctgaaccaaattacttgttttaagattgcaattaatgcttgcttctgatgcttttgtctaatggttttaaataactgcag
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 6
GGTTGCTCCAAAATCAACACTTGGTAATTGGATGAACGAAATTCGCCGGTTTTGTCCTGTCCTACGTGCTGTGAAGTTCCTTGGTAATCCTGAGGAGAGGgtaagtca--------tgagctgt-ctgccatttcagaatttcatgtaaacgtttatcccaggat----tctgaaatgtctgctaactgatgcag
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GGTTGCTCCAAAATCTACTCTTGGAAATTGGATGAATGAGATTCGGCGCTTTTGTCCTGTTCTTCGTGCAATCAAGTTTCTTGGCAACCCCGATGAAAGGgtaagaccatctttactgagttgaattattgtggcaaaggttacagttgatgcttaatttgaactgtttttcctaatggttttgacttgctacag
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 6
GGTTGCTCCAAAATCAACACTTGGTAATTGGATGAACGAAATTCGCCGGTTTTGTCCTGTCCTACGTGCTGTGAAGTTCCTTGGTAATCCTGAGGAGAGGgtaag--------tcatgagctgt-ctgccatttcagaatttcatgtaaacgtttatcccaggat----tctgaaatgtctgctaactgatgcag
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GGTTGCTCCAAAATCTACTCTTGGAAATTGGATGAATGAGATTCGGCGCTTTTGTCCTATTCTTCGTGCAATTAAGTTTCTTGGCAACCCTGATGAAAGGgtaagaccatcttttctgggttgaattattgtggcaaaggttacaattgatgcttaatttgaactgtttttcctaatggttttgacttgctgcag
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 6
GGTTGCTCCAAAATCAACACTTGGTAATTGGATGAACGAAATTCGCCGGTTTTGTCCTGTCCTACGTGCTGTGAAGTTCCTTGGTAATCCTGAGGAGAGGgtaagtcatgagctgtctgccatttcag-aatttcatgtaaacgttta---tcccaggattctgaaatgtctgctaactgatgcag
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TGTTGCCCCAAAATCGACTCTTGGCAACTGGATGAATGAAATTCGACGTTTTTGTCCAGTTCTGCGTGCTGTGAAGTTTCTTGGAAATCCTGATGAAAGGgtgtgtcattcaggccctgctttcagagtaattctttttttatttacagttttccactgcactttgctaacacttcgtctctgcagMapped 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|116481378|gb|EG523970.1|EG523970EST: TTTGTCCTGTCCTACGTGCTGTGAAGTTCCTTGGTAATCCTGAGGAGAGG AGACATATTCGAGAAGACCTGCTAGTTGCTGGGAAATTTGATATTTGTGTC
genomic: TTTGTCCTGTCCTACGTGCTGTGAAGTTCCTTGGTAATCCTGAGGAGAGGgtaagtcatg ... actgatgcagAGACATATTCGAGAAGACCTGCTAGTTGCTGGGAAATTTGATATTTGTGTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGTTGCTCCAAAATCAACACTTGGTAATTGGATGAACGAAATTCGCCGGTTTTGTCCTGTCCTACGTGCTGTGAAGTTCCTTGGTAATCCTGAGGAGAGGgtaagtcatgagctgtctgccatttcagaatttcatgtaaacgtttatcccaggattctgaaatgtctgctaactgatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG