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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCACCAGCCACCCAACCTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtag

Basic information

species Oryza sativa
transcript LOC_Os09g38790.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g38790.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G081812_T01 (Zea mays), 5'ss of exon 5
AGCGGCTGTACCTCCACCCGCT---TCTAATAATAAAGCACCAGCCACCCAACCTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttccatcctctctttagttgttattctcattagagatcatttggtatata-tgttacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtag
    | || | || |||| ||    || |||||||| ||  | |   ||||||| | | | ||||| || |||||||||||||||||||||||||||||||||||||  || | | ||    | ||  |||  ||        || | | ||| |  |||  | || || | | || |||   || |   | ||||||| | |||| || ||| |||||
---AGTTGGATCTTCACCTGCAGTATCCAATAATAAGGCGTCTGGTGCCCAACCAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgctt-ctaaccatcatctatatgtctttt-------agtttacttg-tgcatagcgatatatgatt-gaaatg---ttaa---taatctcaattttttgctgtcttttgtag
















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|88589372|gb|CI707242.1|CI707242
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTACC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|29680885|gb|CB677160.1|CB677160
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|38475380|gb|CF959513.1|CF959513
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCCATGATGAAACTAG
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGC-ATGATGAAACTAG
EST: gi|88588125|gb|CI705920.1|CI705920
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAACATTGTCGCTACCCACCTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|88436645|gb|CI691377.1|CI691377
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAACCAATGTCAATG                         GAGGAAAGAAGATNGTCGCTACCCAAGTATCAGGTGCATGATGAA
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAA
EST: gi|25797175|gb|CA753136.1|CA753136
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GGAGGAAAGAAGATTGTCGCTACCCCAGGTATCAGGTGCATGATGANACTA
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagG-AGGAAAGAAGATTGTCGCTACCCAAG-TATCAGGTGCATGATGAAACTA
EST: gi|95100848|gb|CI692566.1|CI692566
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTACC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|33679167|gb|CF307406.1|CF307406
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|88584106|gb|CI701634.1|CI701634
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTA
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTA
EST: gi|88586844|gb|CI704565.1|CI704565
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTACC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|95101217|gb|CI692956.1|CI692956
EST:     CTGCTGCAAATGAAGTCTATCTGGTGTGGGATGATGAACCAATGTCAATG                         GAGGAAAGAAGATCGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|29624560|gb|CB629571.1|CB629571
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|88386761|gb|CI682916.1|CI682916
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTACC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|88584300|gb|CI701845.1|CI701845
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCCAAGTATCAGGTGCATGATGAAACTAG
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCC-AAGTATCAGGTGCATGATGAAACTAG
EST: gi|88590829|gb|CI707721.1|CI707721
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|29680924|gb|CB677199.1|CB677199
EST:     CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATG                         GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC
genomic: CTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttc ... acttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCACCAGCCACCCAACCTGGTGCAAATGAAGTCTATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatattttccatcctctctttagttgttattctcattagagatcatttggtatatatgttacattactagatatgagtttgagggttatctcaaatatttgttgacttgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA