Sequence
atgc intronic sequence ATGC exonic sequence...ctgactaggagtaggagttcgtttttgtcatccatgtgacatagattttctgctagcaaaaaggatgtgaggaacactattaattttttgtttccttcagCGCTGCTGTAAATGCAGAGACAGGCGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTCGACAACAGAATAGATGCCAAAAGGACCTTACGGGAAATT
Basic information
species | Glycine max |
transcript | GLYMA16G03670.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 1
ctgactaggagtaggagttcgtttttgtcatccatgtgacatagattttctgct--agcaaaaaggatgtgaggaacactattaattttttgtttccttc----agCGCTGCTGTAAATGCAGAGACAGGCGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTCGACAACAGAATAGATGCCAAAAGGACCTTACGGGAAATT
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----gtgggggaaatgggtcacggcggcc-caaaaatgttatggtttgactgcttgagtagatgtgat-tatattgtagtagtaattttgtttttcctatttgtagCGCGGCTGTTAACTCGGAGAACGGCGAGGAAGTTGCCATCAAGAAGATTGGCAATGCATTCGACAACCATATCGATGCCAAGCGGACACTGAGAGAAATC
upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 1
ctgactaggagtaggagttcgtttttgtcatccatgtgacatagattttctgcta-gcaaaaaggatgtgaggaacactattaattttttgtttccttcagCGCTGCTGTAAATGCAGAGACAGGCGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTCGACAACAGAATAGATGCCAAAAGGACCTTACGGGAAATT
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-aagggcacaatagaagctacacaatttcatctaattgacttcatttctctgttttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT
upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ22596 (Selaginella moellendorffii), 3'ss of exon 1
ctgactaggagtaggagttcgtttttgtcatccatgtgacatagattttctgctagcaaaaaggatgtgaggaacactat-taattttttgtttccttca--gCGCTGCTGTAAATGCAGAGACAGGCGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTCGACAACAGAATAGATGCCAAAAGGACCTTACGGGAAATT
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------gtgagtgtgctccttcctccgtctcccaattggggtcgatttgccccttgcct---gctctcaaagctcgccgtctcataccaagtttcacgcacagCTCTGCAGTGAACAGCGAGACCAACGAAGAAGTTGCTATCAAGAAAATCGGCAATGCCTTCGACAACAGGATCGATGCCAAGCGCACATTGCGCGAGATCMapped 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|23052819|gb|BU577310.1|BU577310EST: TATGTCCCTCCTATTCGCCCTGTCGGTAGAGGTGCTTATGGTATTGTTTG CGCTGCTGTAAATGCAGAGACAGGCGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TATGTCCCTCCTATTCGCCCTGTCGGTAGAGGTGCTTATGGTATTGTTTGgtaagcccag ... tttccttcagCGCTGCTGTAAATGCAGAGACAGGCGAGGAAGTTGCCATTAAGAAGATTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctgctagcaaaaaggatgtgaggaacactattaattttttgtttccttcagCGCTGCTGTAAATGCAGAGACAGGCGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTCGACAACAGAATAGATGCCAAAAGGACCTTACGGGAAATT
tattaat putative branch site (score: 2)
ttttttgtttccttc CT-rich tract
aacactattaattttt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgactaggagtaggagttcgtttttgtcatccatgtgacatagattttctgctagcaaaaaggatgtgaggaacactattaattttttgtttccttcagCGCTGCTGTAAATGCAGAGACAGGCGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTCGACAACAGAATAGATGCCAAAAGGACCTTACGGGAAATT
ctgacta
- - - - - - - - - - - - - -tcatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - agcaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatgtg