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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggttttttctggttgttcttgcgattcttgcttcggggtgtagtggatctgatactgctgagttcgtcgattcgatgtatatctgctaatccgt...

Basic information

species Oryza sativa
transcript LOC_Os01g68710.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68710.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G153991_T01 (Zea mays), 5'ss of exon 2
CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggttttttctggttgttcttgcgattcttgcttcggggtgtagtggat-ctgatactgctgagttcgtcg-attcgatgtatatctgctaatccgt---
| ||||||||||||||||| || ||||| |||||||||||||| || |||||   | ||  |   |    |   |  | | |||     |  | |  | ||  | |||     || || |  | || ||      |    | | |  | | |   
CGTCGGCCAAGAAGTCCGGCGACGTCACCGAGCTTCAGATCGGCGTCAAGgt---ctgtgctccgtaaccgcggt--caactctcctcgccagtttaattgtttgctgtcttcgcggattctggcggatcttggattcgccggtttcttcattta

upper sequence: LOC_Os01g68710.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G031204_T01 (Zea mays), 5'ss of exon 2
CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggttttt--tctggttg-ttcttgcgattcttgcttcggggtgtagtggatctgatactgctgagttcgtcgattcgatgtatatctgctaatccgt
| ||||||||||||||| | || ||||| |||||||||||||| || |||||  | | | | |   | |||   ||||  | |   ||   | |     ||      | ||| |||  |  |  |  |||| |  |    | | |   | |||
CGTCGGCCAAGAAGTCCAGCGACGTCACCGAGCTTCAGATCGGCGTCAAGgtgtctgctctgtaaccgggtcaattctctccaccatttaattgcctgttatccttgcggattctggcggatctgg-gattagccgccggttttc--gttcgt
















Mapped 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|88723075|gb|CI746585.1|CI746585
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|51946051|gb|CV152392.1|CV152392
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|55440369|gb|CV733494.1|CV733494
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCATAACTGNGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|88723491|gb|CI747001.1|CI747001
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|55409944|gb|CV722320.1|CV722320
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|88723609|gb|CI747119.1|CI747119
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|88722134|gb|CI745461.1|CI745461
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|568861|gb|D39710.1|D39710
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|33659572|gb|CF282185.1|CF282185
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|163923518|gb|EG711137.1|EG711137
EST:     TCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCATATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: TCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|88344739|gb|CI624390.1|CI624390
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGAAAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|88723542|gb|CI747052.1|CI747052
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|86829242|gb|CI284927.1|CI284927
EST:     GATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: GATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|11171677|gb|AU163906.1|AU163906
EST:     TTCGGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: TTC-GGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|55436954|gb|CV731666.1|CV731666
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|58589883|gb|CF988191.1|CF988191
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|55433322|gb|CV729734.1|CV729734
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|88726773|gb|CI750428.1|CI750428
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|55413431|gb|CV725807.1|CV725807
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTG-AN                         NNNNNNCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|2442348|gb|C74119.1|C74119
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|55414253|gb|CV726629.1|CV726629
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTTTGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|55412950|gb|CV725326.1|CV725326
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|88827090|gb|CI777655.1|CI777655
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|2442460|gb|C74231.1|C74231
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|55441436|gb|CV734038.1|CV734038
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|33685240|gb|CF313479.1|CF313479
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|55413109|gb|CV725485.1|CV725485
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|163928575|gb|EG711160.1|EG711160
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
EST: gi|428562|gb|D24714.1|D24714
EST:     CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTNAAG                         TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA
genomic: CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... ctcctttcagTACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCGGCCAAGAAGTCCGGAGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggttttttctggttgttcttgcgattcttgcttcggggtgtagtggatctgatactgctgagttcgtcgattcgatgtatatctgctaatccgt

- - - - AAGAAG
- - - -  AGAAGT
- - - - - - - -  GGAGAT
- - - - - - - - - GAGATG
- - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - -  GAGCTT