Sequence
atgc intronic sequence ATGC exonic sequencegtatacttagcaagaatttaacctgtcctgcagaaaccttttttaattttaagttggtttgactaatactatttacttatatattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTATTAGATATTACTGACTTTTCTGTGAAG
Basic information
species | Glycine max |
transcript | GLYMA09G23250.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 2
-------gtatacttagcaagaatttaacctgtcctgcagaaaccttttttaattttaagttggtttgactaatactatttacttatatattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTATTAGATATTACTGACTTTTCTGTGAAG
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gtaaatcatattccattgcacaggttaaggagt--tgctgaatcactcttct-tctggccctgactaagttaaggctaattaagttcctatcttgaagAACTTTACCAGCAAATGCTTGCCAAAGCGCTTGCCCACTATTTTGAAGCAAAATTGCTGTTGCTAGATCCTACAGATTTTCTCATAAAG
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 3
------------------gtatacttagcaagaattta---acctgtcctgcagaaaccttttttaattttaagttggtttgactaatactatttacttat--------atattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTATTAGATATTACTGACTTTTCTGTGAAG
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gtatgctctctggaatatgttctctgaccctgcatttggatatttatgtttctgagtccttttgatggcctaacttg-tttgccttttgctttacttttatttttgttaatcttttgaagAACTTTACCAGCAAACACTTGCCAAAGCTTTAGCACATTTCTTTGAAGCAAAGTTGCTGCTATTGGATGTTAATGACTTTTCTCTAAAG
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g01840.t01 (Vitis vinifera), 3'ss of exon 3
gtatacttagcaaga-atttaacctgtcctgcagaa--accttttttaat--tttaagttggtttgact-----------------aatactatttacttatatattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTATTAGATATTACTGACTTTTCTGTGAAG
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gtatgttgtctggaatatgtgatctgatatggatatttatgtttcttagtccttttaattggcccaatttggttgccttttgcttcatttttattcttgtttatcttctgaagAACTTTATCAGCGAGCACTCGCCAAAGCTTTAGCACAATTCTTTGAAGCAAAGTTGCTGCTGTTGGATGTTAATGACTTTTCTCTAAAGMapped 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|213610767|gb|DB963139.1|DB963139EST: CAGGAACCTCCCACCAGCAAGCAGGGCTATTTTGCTATCTGGTCCAGCAG AACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAA
genomic: CAGGAACCTCCCACCAGCAAGCAGGGCTATTTTGCTATCTGGTCCAGCAGgtatacttag ... tattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttttttaattttaagttggtttgactaatactatttacttatatattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTATTAGATATTACTGACTTTTCTGTGAAG
gactaat putative branch site (score: 2)
tttgactaatactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatacttagcaagaatttaacctgtcctgcagaaaccttttttaattttaagttggtttgactaatactatttacttatatattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTATTAGATATTACTGACTTTTCTGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT