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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGCTAGGACTCACCAAGGCTATTGGTGTTAGCAACTTCAGTTGCAAGAAGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttccaaacattcctatacattataataatcttgactcttttggaattgcatctatatatataccatcaactagagaaaaacccattagcatta...

Basic information

species Oryza sativa
transcript LOC_Os10g02480.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g02480.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv05s0077g02150.t01 (Vitis vinifera), 5'ss of exon 2
AAGGCTAGGACTCACCAAGGCTATTGGTGTTAGCAACTTCAGTTGCAAGAAGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgta--aaagttccaaacattcctatacattataataatcttgactcttttggaattgcatctatatatataccatcaactagagaaaaacccattagcatta
 ||  | ||  |  ||||  ||||||| || ||||||||||||||||||||||||       | |||   |  ||  ||||| ||||||| |  ||||| |||  |||          | || |  |   ||||||  |    ||  ||    | |  ||    | ||  | |      |  ||                  
CAGATTGGGCTTAGCCAAATCTATTGGAGTCAGCAACTTCAGTTGCAAGAAGCTCTCCCAGCTTCTCCAGTATGCTGCCATCCCTCCTGCCGTTAATCAGgtattaaaacagggggtgtgccgaggc---ataataggcagagctagttcatgagttgatgatgaaattgaacgcgtgtttcag------------------

upper sequence: LOC_Os10g02480.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv05s0077g02180.t01 (Vitis vinifera), 5'ss of exon 3
AAGGCTAGGACTCACCAAGGCTATTGGTGTTAGCAACTTCAGTTGCAAGAAGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttccaaacattcctatacattataataatcttgactcttttggaattgcatctatatatataccatcaactagagaaaaacccattagcatta
 ||  | || ||  ||||| ||||||| || ||||||||||||||||| ||||||       | |||   |  || || ||| ||||||| |  |||||       ||| | ||||  | | | |  ||  |||||   ||       || | | |||   |  ||  |  || || | ||  |       | ||     
CAGATTGGGCCTAGCCAAGTCTATTGGCGTAAGCAACTTCAGTTGCAAAAAGCTCTCTCAGCTTCTCCAATATGCTACTATCCCTCCTGCTGTTAATCAG-
















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|29639000|gb|CB644009.1|CB644009
EST:     AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAA                         GTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
genomic: AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
EST: gi|29615189|gb|CB620202.1|CB620202
EST:     AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAA                         GTTGAGGTGCATCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
genomic: AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
EST: gi|8859367|gb|AU096685.1|AU096685
EST:     AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAA                         GTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
genomic: AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
EST: gi|33800272|gb|CF326002.1|CF326002
EST:     AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAA                         GTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
genomic: AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
EST: gi|29638999|gb|CB644008.1|CB644008
EST:     AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAA                         GTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
genomic: AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
EST: gi|29688767|gb|CB685042.1|CB685042
EST:     AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAA                         GTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
genomic: AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
EST: gi|29688766|gb|CB685041.1|CB685041
EST:     AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAA                         GTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
genomic: AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
EST: gi|88965301|gb|CI009337.1|CI009337
EST:     CTGCAGCAAATCAA                         GTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
genomic: CTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
EST: gi|25798126|gb|CA754094.1|CA754094
EST:     AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAA                         GTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCCAA
genomic: AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGC-AA
EST: gi|2801031|gb|AA754325.1|AA754325
EST:     AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAA                         GTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
genomic: AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
EST: gi|38471635|gb|CF955766.1|CF955766
EST:     AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAA                         GTTGAGGTGCATCCTTACTGTCGGCAAAAT
genomic: AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAAT
EST: gi|29686964|gb|CB683239.1|CB683239
EST:     AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAA                         GTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG
genomic: AGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttc ... acacttgcagGTTGAGGTGCACCCCTACTGTCGGCAAAATAAATTGAGGGAGTTCTGCAAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGCTAGGACTCACCAAGGCTATTGGTGTTAGCAACTTCAGTTGCAAGAAGCTCGAGACATTGCTCTCCTTCGCAACCATCTCTCCTGCAGCAAATCAAgtaaaagttccaaacattcctatacattataataatcttgactcttttggaattgcatctatatatataccatcaactagagaaaaacccattagcatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG