Sequence
atgc intronic sequence ATGC exonic sequence...tttttaactattaaggattatgtggtaggtaggttgagtactgtttttcgatatttatggatgttgagtgttgactacataaatattttatgtattatagGATGGGCGTCGGGTACACGTCATTGAAAGAGACCTGAGTGAGCCTGATCGAATTGTTGGAGAGTTGCTTCAACCCGGTGGCTATCTCAAATTAATTGAGC
Basic information
species | Glycine max |
transcript | GLYMA0041S00260.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA0041S00260.3 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g08550.t01 (Vitis vinifera), 3'ss of exon 1
tttttaacta--ttaaggattatgtggtaggtaggttgagtactgtttttcgatatttatggatgttgagtgttgactacataaatattttatgtattatagGATGGGCGTCGGGTACACGTCATTGAAAGAGACCTGAGTGAGCCTGATCGAATTGTTGGAGAGTTGCTTCAACCCGGTGGCTATCTCAAATTAATTGAGC
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gccttaacaaagtcagagtcgctgtaatagg--ggttaaaaaaaggacattctaatgcaatttggcttcttctttacctaataattcaagtctttatttcagGATGGGCGTAGGGTACGCGTGATTGAAAGAGACTTAACTGAGCCTGACCGAATTGTTGGTGAACTGCTACAGCCAGGGGGCTACCTCAAATTGATTGAGT
upper sequence: GLYMA0041S00260.3 (Glycine max), 3'ss of exon 1
lower sequence: EFJ23930 (Selaginella moellendorffii), 3'ss of exon 1
tttttaactattaaggattatgtggtaggtaggttgagtactgtttttcgatatttatggatgttgagtgttgactacataaatattttatgtattatagGATGGGCGTCGGGTACACGTCATTGAAAGAGACCTGAGTGAGCCTGATCGAATTGTTGGAGAGTTGCTTCAACCCGGTGGCTATCTCAAATTAATTGAGC
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-------------------------------------gtgatttctttccagctctaaaaaaaatctgtgttta----acagccatta--------acagGATTCGCGAAGAGTTTTGTTGATCGAGAGGGATTGTTCCGAGCCGGATAGAATCGTTGGAGAGCTGCTACAACCCGGTGGCTATCTCAAGCTCGTGGAGC
upper sequence: GLYMA0041S00260.3 (Glycine max), 3'ss of exon 1
lower sequence: EFJ21553 (Selaginella moellendorffii), 3'ss of exon 1
tttttaactattaaggattatgtggtaggtaggttgagtactgtttttcgatatttatggatgttgagtgttgactacataaatattttatgtattatagGATGGGCGTCGGGTACACGTCATTGAAAGAGACCTGAGTGAGCCTGATCGAATTGTTGGAGAGTTGCTTCAACCCGGTGGCTATCTCAAATTAATTGAGC
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-------------------------------------gtgattcctttccagctctaaaaaaaatctgtgttta----acagccatta--------acagGATTCGCGAAGAGTTTTGTTGATCGAGAGGGATTGTTCCGAGCCGGATAGAATCGTTGGAGAGCTGCTACAACCCGGTGGCTATCTCAAGCTCGTGGAGCMapped 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|209715569|gb|BW657362.1|BW657362EST: TTGTCGGAGCCGGCGTCGCCGGCGCCTCTCTGGCGCACACTCTCGGCAAG GATGGGCGTCGGGTACACGTCATTGAAAGAGACCTGAGTGAGCCTGATCGA
genomic: TTGTCGGAGCCGGCGTCGCCGGCGCCTCTCTGGCGCACACTCTCGGCAAGgtaggtttga ... tgtattatagGATGGGCGTCGGGTACACGTCATTGAAAGAGACCTGAGTGAGCCTGATCGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcgatatttatggatgttgagtgttgactacataaatattttatgtattatagGATGGGCGTCGGGTACACGTCATTGAAAGAGACCTGAGTGAGCCTGATCGAATTGTTGGAGAGTTGCTTCAACCCGGTGGCTATCTCAAATTAATTGAGC
tgttgac putative branch site (score: 3)
ttgactacataaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttaactattaaggattatgtggtaggtaggttgagtactgtttttcgatatttatggatgttgagtgttgactacataaatattttatgtattatagGATGGGCGTCGGGTACACGTCATTGAAAGAGACCTGAGTGAGCCTGATCGAATTGTTGGAGAGTTGCTTCAACCCGGTGGCTATCTCAAATTAATTGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA