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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCGGCCTGGGCATGGCCGCTCGTCTTCCTCGTCTCGTGCTGCTGTTCTTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgctggggaaaaggaaaaaaagaagaagaaaatctctgtttgggttggggtctcattgtttgcttgcttgtgcttgtgcttttcttttttgttt...

Basic information

species Oryza sativa
transcript LOC_Os10g25090.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G004572_T01 (Zea mays), 5'ss of exon 1
---ATGGCGGCCTGGGCATGGCCGCTCGTCTTCCTCGTCTCGTGCTGCTGTTCTTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgctggggaaaaggaaaaaaagaagaagaaaatctctgtttgggttggggtctcattgtttgcttgcttgtgcttgtgcttttcttttttgttt---------
   |  |||||||||||      |||  || |||||    |||||| | |  ||||||||| ||||| |||||||||||||||  |||| ||||| |||||||||  ||     |  | |  || ||         |    | |||| | |  ||   | ||  |  ||  | | ||  || || |   || ||    || ||         
GCGACAGCGGCCTGGGCCGCATGGCTGCTCATCCTCA---CGTGCTTCGGCGCTTGGACCCCGCGGCAAATCTTGGTTGCTGCAGCCACCGACGCGAATGATGgtaggc-----gatacactgagaatcttgccttg----tttctgatcgcatttctgccttctctttctccttctcatgtttcttggttgctgcgctgcttccttctatg
















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|88369294|gb|CI577757.1|CI577757
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88311529|gb|CI572585.1|CI572585
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCAACAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|86888413|gb|CI303695.1|CI303695
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCCATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88449338|gb|CI582210.1|CI582210
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88730221|gb|CI753836.1|CI753836
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88385785|gb|CI566647.1|CI566647
EST:     ATGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88406193|gb|CI593973.1|CI593973
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|6507597|gb|AU064258.2|AU064258
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88298922|gb|CI567925.1|CI567925
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88720186|gb|CI743485.1|CI743485
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGAACACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88298740|gb|CI565937.1|CI565937
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88371283|gb|CI600131.1|CI600131
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGAACACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88314468|gb|CI604952.1|CI604952
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88422824|gb|CI573986.1|CI573986
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88428401|gb|CI564869.1|CI564869
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88392563|gb|CI625385.1|CI625385
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88721915|gb|CI743427.1|CI743427
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88425544|gb|CI569268.1|CI569268
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88395348|gb|CI611265.1|CI611265
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88385459|gb|CI564119.1|CI564119
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88402885|gb|CI613333.1|CI613333
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTACTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88368294|gb|CI577565.1|CI577565
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88300565|gb|CI587369.1|CI587369
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88401962|gb|CI593674.1|CI593674
EST:     TGGACCCAGCGGCGAATCTTGGTTTGCTGCGACCACTGACGCCAATGATG                         TTACTTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTG
genomic: TGGACCCAGCGGCGAATCTTGG-TTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTAC-TGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTG
EST: gi|88405784|gb|CI609683.1|CI609683
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|29631005|gb|CB636014.1|CB636014
EST:     GCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: GCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88430712|gb|CI596826.1|CI596826
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88412193|gb|CI573469.1|CI573469
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88415116|gb|CI583939.1|CI583939
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88396144|gb|CI595692.1|CI595692
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88426869|gb|CI584232.1|CI584232
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
EST: gi|88314779|gb|CI608238.1|CI608238
EST:     TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATG                         TTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC
genomic: TTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 70 (downstream exon)
Score: 6

ATGGCGGCCTGGGCATGGCCGCTCGTCTTCCTCGTCTCGTGCTGCTGTTCTTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgct ... tattatgcagTTACTGTCCTCAATGCGCTATTCACCAGCCTCAATTCGCCGGGGCAGCTGCGCGGTTGGCAGGTGAATGGCGGTGACCCATGTGGCGCCTCATGGCAGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGCGGCCTGGGCATGGCCGCTCGTCTTCCTCGTCTCGTGCTGCTGTTCTTGGACCCAGCGGCGAATCTTGGTTGCTGCGACCACTGACGCCAATGATGgtgagctgctggggaaaaggaaaaaaagaagaagaaaatctctgtttgggttggggtctcattgtttgcttgcttgtgcttgtgcttttcttttttgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa