Sequence
atgc intronic sequence ATGC exonic sequence...agccagtcatttttgcattttttatttggtcatgtcattttcctgttttttatattgtatttgtttgtcaactgaatgtttctgccaatgtaatttctagGTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTATTGGAAATATGCTCAGTGTCCAG
Basic information
species | Glycine max |
transcript | GLYMA03G40600.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g56620.1 (Oryza sativa), 3'ss of exon 3
agcca-gtcatttttgca-ttttttatttggtcatgtcattttcctgttttttatattgtatttgtttgtcaactgaatgt-ttctgcca------------atgtaattt-----ctagGTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTATTGGAAATATGCTCAGTGTCCAG
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-gttatgtcatctgttcagtttcatgcctaactactattgtgcccgatcatctttattctgttcgtgtaagaatgcaaagcactgcaccgttgacttacagtatgtaattcacataccagGTTTCATCTTTACAAGGAGAACAAGGACACCCAAGAGGCACTAGGAAAGATAGGCAAGATGCTAGGGCTTCAG
upper sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G04820.1 (Arabidopsis thaliana), 3'ss of exon 4
agccagtcatttttgcattttttatttggtcatgtcattttcctgtt----ttttatattgtatttgtttgtcaactgaatgtttctgccaatgtaatttctagGTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTATTGGAAATATGCTCAGTGTCCAG
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---tattttatacatcataatctctgtagtgcttttattttattaatgcatttggacgttcaacctatgtgtcatttgatt-tatgagtcgtttaagttaatagGTTCCATCTTTACAAGGAGAACAAAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAG
upper sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g01840.t01 (Vitis vinifera), 3'ss of exon 4
agccagtcatttttgcattttttatttggt---catgtcattttcctgttttttatattgtatttgtttgtcaactgaatgtttctgccaatgtaa-tttctagGTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTATTGGAAATATGCTCAGTGTCCAG
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----gcttctgaaaacatttttttttcaacttccattgatctttcattgcatcaactttgcacttgaacactatctgattagtactgtcagtataaattttcagGTTTCATCTTTACAAGGAGAACAAGGATACCCAGGAGGCCATAGGATTGATTGGAAAGATGCTGGGCATCCAGMapped 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|24205460|gb|BU964713.1|BU964713EST: GACAGCCGAGGTTCAGAAAATTGGCCTAAAAATGTTGGCAAGTTCCTTAG GTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTAT
genomic: GACAGCCGAGGTTCAGAAAATTGGCCTAAAAATGTTGGCAAGTTCCTTAGgtaatattgc ... taatttctagGTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTAT
EST:
gi|208046299|gb|GD848687.1|GD848687EST: TTGGCCTAAAAATGTTGGCAAGTTCCTTAG GTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTAT
genomic: TTGGCCTAAAAATGTTGGCAAGTTCCTTAGgtaatattgc ... taatttctagGTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttatattgtatttgtttgtcaactgaatgtttctgccaatgtaatttctagGTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTATTGGAAATATGCTCAGTGTCCAG
tttct CT-rich tract
tatattgtatttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agccagtcatttttgcattttttatttggtcatgtcattttcctgttttttatattgtatttgtttgtcaactgaatgtttctgccaatgtaatttctagGTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTATTGGAAATATGCTCAGTGTCCAG
- ccagtca
- - - - - - -tgcattt
- - - - - - - - - - - - - - -tcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgccaa