Sequence
atgc intronic sequence ATGC exonic sequence...taatgtagctaacctcatctaatgggaaaaggcttttgttgttgatgtagtttaaatacgtatttgttaatcatttatatttgtgtctttactccctcagGTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCATCTA
Basic information
species | Glycine max |
transcript | GLYMA20G32200.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G157437_T01 (Zea mays), 3'ss of exon 1
taatgtagctaacctcatctaatgggaaaaggcttttgttgttgatgtagtttaaatacgtatttgttaatcatttatatttgtgtctttactccctcagGTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCATCTA
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----gtaattattgtgttcttagctccccacccccctagaatatgtactcccttga-aggtaatattttaccgctatcttttgcactggtatttt-tcagGTGATGGCAATCAGTGAGTCATCAAGATTGCATTCTTCGTTGCAAAAGGAAAGTGTTCCTATAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAA
upper sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 8
taatgtagctaacctcatctaatgggaaaaggcttttgttgttgatgtagtttaaatacgtatttgttaatcatttatatttgtgtctttactccctcagGTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCATCTA
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----gtaactattgtgttcttagctccccacccccctagaatatgtactcccttga-aggtaatattttactgctatcttttgcactggtatttt-tcagGTGATGGCAATCAGTGAGTCATCAAGACTGCATTCTTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAA
upper sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 8
------------------------------------taatgtagctaacctcatctaatgggaaaaggcttttgttgttgatgtagtttaaatacgtattt-gttaatcatttatatttgtgtctttactccctcagGTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCATCTA
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gtaatatctaccacatgcatctccttgatgtcctcctatcttcaagaataaaatccattggctgagaacttccgtccaatgttggtcttaagttggcatctcactgctcattactttttgt---ttatctcataaagGTAATGGCTGTCAGCGAGTCTTCTAGGTTAAGTGCTTCCTTGAAGAAGGAAAGTGTTCCCGTCAAAAGACTCATTGTTAATCAGCTTCTCCCGCCATCCT
upper sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 9
taatgtagctaacctcatctaatgggaaaaggcttttgttgttgatgtagtt-taaatacgtatttgttaatcatttat--atttgtgtctttactccctcagGTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCATCTA
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-attagctcttttatgggttatctgtagtaaa--tcagttgtaaagaaagttattaatttgtacttctaaataagctactcacttccaatttcttcatccaagGTGATGGCGATTAGTGAGTCATCAAGGTTACATGCTTCCTTGAAGAGGGAAAATGTTCCTGTCAAGAAGCTAATAGTCAATCAGGTTCTTCCCCCATCTAMapped 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|208341366|gb|GE134120.1|GE134120EST: TCTTTCGTGATACTGATTCGACCGAATTTGTCATTGTTACAATCCCCACG GTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAA
genomic: TCTTTCGTGATACTGATTCGACCGAATTTGTCATTGTTACAATCCCCACGgtatgactta ... actccctcagGTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAA
EST:
gi|193404452|gb|FK365361.1|FK365361EST: TTCGACCGAATTTGTCATTGTTGCAATCCCCACG GTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAA
genomic: TTCGACCGAATTTGTCATTGTTACAATCCCCACGgtatgactta ... actccctcagGTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtagtttaaatacgtatttgttaatcatttatatttgtgtctttactccctcagGTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCATCTA
tgttaat putative branch site (score: 3)
tgtctttactccctc putative PPT
tttaaatacgtatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatgtagctaacctcatctaatgggaaaaggcttttgttgttgatgtagtttaaatacgtatttgttaatcatttatatttgtgtctttactccctcagGTGATGGCAATTAGTGAGTCATCTAGATTGAGTGCTTCCCTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCATCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA