Sequence
atgc intronic sequence ATGC exonic sequenceCCTTTACAGTGATTATCTCGATGCTGCTGATACACCTGGATGGTATTGTGGACCCAATTTCTTCTCAACTGATGTTCTTCGAGACTTTGCAAAGACCCAGgtgggtgctagttttctgctccataataataatgatgatgtaatacaagtgtctgggctaataatctttctctgtcttggtgattttgtag
Basic information
species | Glycine max |
transcript | GLYMA07G40090.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G40090.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g52630.2 (Oryza sativa), 5'ss of exon 4
CCTTTACAGTGATTATCTCGATGCTGCTGATACACCTGGATGGTATTGTGGACCCAATTTCTTCTCAACTGATGTTCTTCGAGACTTTGCAAAGACCCAGgtgggtgctagttttctgctccataataataat-gatgatgtaatacaagtgtctgggctaataatctttctctgtcttggtgattttgtag
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TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaaccct--tcaatttgcag
upper sequence: GLYMA07G40090.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G49720.1 (Arabidopsis thaliana), 5'ss of exon 5
CCTTTACAGTGATTATCTCGATGCTGCTGATACACCTGGATGGTATTGTGGACCCAATTTCTTCTCAACTGATGTTCTTCGAGACTTTGCAAAGACCCAGgtg--ggtgctagttttctgctcc--ataataataatgat----gatgtaatacaagtgtctgggctaataatctttctctgtcttggtgattttgtag-------------------------------------------------------------------------
|| |||||||||||||| |||||||||||||| ||||||||||| |||||||| ||||||| || || ||| || || |||||||| | ||||||| | | || | | | ||| | | ||| | || ||| || || | | | | | || ||| || | | |||| |
TCTATACAGTGATTATCTGGATGCTGCTGATACTCCTGGATGGTACTGTGGACCTAATTTCTATTCGACAAGTGTGCTACGTGACTTTGCTAGATCCCAGgtattgcttcttttcctttactctttacagaaatggtaatctcagatatagta-atggataagatccaaaaatgacacttt-taaccaagattgtacgaagatctttttaaactccattttttattttgacatctaaattggatttaactcggccttgctgtattttggcag
upper sequence: GLYMA07G40090.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G24260.1 (Arabidopsis thaliana), 5'ss of exon 5
CCTTTACAGTGATTATCTCGATGCTGCTGATACACCTGGATGGTATTGTGGACCCAATTTCTTCTCAACTGATGTTCTTCGAGACTTTGCAAAGACCCAGgtgggtgctagttttctgctccataataataatgatgatgtaatacaagtgtctgggctaataatctttctctgtcttggtgattttgtag
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ACTATTCAGTGATTATCTAGAGGCTGCTGATACTCCCGGATGGTACTGTGGTCCTAACTTCTATACTACTGAATTCCTACGCAACTTTTCAAGATCGCAGgta-----tgattcacaaatgaaggaaaacaaacaagattttgaaggag---cttatctgatggaactt-tgtgtcttt-tgttttggcag
upper sequence: GLYMA07G40090.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 5
CCTTTACAGTGATTATCTCGATGCTGCTGATACACCTGGATGGTATTGTGGACCCAATTTCTTCTCAACTGATGTTCTTCGAGACTTTGCAAAGACCCAGgtgggtgctagttttctgctccataataataatgatgatgtaatacaagtgtc----tgggctaataatctttctctgtcttggtgattttgtag------------------------------
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CCTGTACAGTGATTATCTTGAAGCTGCTGACACCCCTGGATGGTATTGTGGACCTAATTTCTATTCAACTGAAGTCCTGCGTGAATTTGCCAAGACCCAGgtatgcgata---tctgattcctcaattaaagttgtgagggaacatgagtctgctcatgtagtaataaatattgttggaaccaacaaggtcacttaaatttttcatatctctgaccttctggcagMapped 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|15200976|gb|BI424628.1|BI424628EST: GACCCAATTTCTTCTCAACTGATGTTCTTCGAGACTTTGCAAAGACCCAG ATTGATTACATCCTTGGGAAGAACCCTCGGAAAATGAGCTATGTTGTAGGT
genomic: GACCCAATTTCTTCTCAACTGATGTTCTTCGAGACTTTGCAAAGACCCAGgtgggtgcta ... gattttgtagATTGATTACATCCTTGGGAAGAACCCTCGGAAAATGAGCTATGTTGTAGGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCTTTACAGTGATTATCTCGATGCTGCTGATACACCTGGATGGTATTGTGGACCCAATTTCTTCTCAACTGATGTTCTTCGAGACTTTGCAAAGACCCAGgtgggtgctagttttctgctccataataataatgatgatgtaatacaagtgtctgggctaataatctttctctgtcttggtgattttgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG