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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttgcaccacccctaaaagagaaggaaactgcttttaaaccctttttggggtttaatacgggaagttgagtatttgatatctctgttgaatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAACCTTCAGCTTGAGGCCACAACACAGTTCCGCAAGTTGCTTTCTATAG

Basic information

species Oryza sativa
transcript LOC_Os01g14950.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 1
------tctttgcaccacccctaaaagagaaggaaactgcttttaaaccctttttggggtttaatacgggaagttgagtatttgatatctctgttgaatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAACCTTCAGCTTGAGGCCACAACACAGTTCCGCAAGTTGCTTTCTATAG
|| | ||| | | | || | | | | ||| || | | || | | | | |||| |||| ||| | |||||| |||||||| || |||||| | |||| ||||||||||| || || |||||||||||||||||||| |||||||| ||||||||||| |||||||
ttgacttcctggcaagcttattttcttggtctttatgtggtcatta-ttcagtttaggttcttttagtactaactatatttgtgatg----tgttaaat-tggtagCTTGAAAGCCTCCCAGCTATGGTCAGTGGGGTTTATTCGGATGACAATAACCTTCAGCTTGAGGCCACCACACAGTTTCGCAAGTTGCTATCTATAG

upper sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 1
tctttgcaccacccctaaaagagaaggaaactgcttttaaaccctttttggggttt-aatacgggaagttgagtatttgatatctct---gttgaatgttg-tagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAACCTTCAGCTTGAGGCCACAACACAGTTCCGCAAGTTGCTTTCTATAG
| | || | | | | || || ||| | ||| ||| | | | | | |||||| | | ||| | ||| ||||| |||||||| || |||||| || |||| ||||||||||| ||||| |||||||||||||||||||| |||||||||||||| ||||| |||||||
-----aagtctactacaatatattgttatgtgtccgttgtacaatttaggttcttttggtaccgacaatacatgctctgatatttgttgtgttataaattggtagCTTGAAAGCCTCCCAGCTATGGTTAGTGGGGTTTATTCGGATGATAATAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG
















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|58682672|gb|CK071359.1|CK071359
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58690748|gb|CK079435.1|CK079435
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAATAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|33678037|gb|CF306276.1|CF306276
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|29662761|gb|CB659036.1|CB659036
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|88362748|gb|CI608897.1|CI608897
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58668036|gb|CK056722.1|CK056722
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58669030|gb|CK057716.1|CK057716
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|88369398|gb|CI580420.1|CI580420
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAA
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|29622103|gb|CB627114.1|CB627114
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|88721733|gb|CI745032.1|CI745032
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAAC
EST: gi|58657036|gb|CK045716.1|CK045716
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|29677816|gb|CB674091.1|CB674091
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58676136|gb|CK064823.1|CK064823
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58676728|gb|CK065415.1|CK065415
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58676970|gb|CK065657.1|CK065657
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|29662174|gb|CB658449.1|CB658449
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|29680121|gb|CB676396.1|CB676396
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58684235|gb|CK072922.1|CK072922
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|29633763|gb|CB638772.1|CB638772
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|29629650|gb|CB634659.1|CB634659
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|33795122|gb|CF323434.1|CF323434
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|29676485|gb|CB672760.1|CB672760
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|88433725|gb|CI582047.1|CI582047
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|88405699|gb|CI609598.1|CI609598
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|29681891|gb|CB678166.1|CB678166
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58675322|gb|CK064009.1|CK064009
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58680439|gb|CK069126.1|CK069126
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58670840|gb|CK059526.1|CK059526
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58681521|gb|CK070208.1|CK070208
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|58689500|gb|CK078187.1|CK078187
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAATAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|29677719|gb|CB673994.1|CB673994
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
EST: gi|88403709|gb|CI611364.1|CI611364
EST:     AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAG                         CTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC
genomic: AGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAAC

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: 52 (upstream exon), 75 (downstream exon)
Score: 56

CAAGAGCCGCCGCGAGGAGAGCCTCCTCAAGAAGCGCCGCGAGGGGCTCCAGGCCCAGGCCCCCGTCCCCGCCTCCGCCGCAACCGGCGTCGATAAGAAGgtgagtagta ... aatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAACCTTCAGCTTGAGGCCACAACACAGTTCCGCAAGTTGCTTTCTATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggggtttaatacgggaagttgagtatttgatatctctgttgaatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAACCTTCAGCTTGAGGCCACAACACAGTTCCGCAAGTTGCTTTCTATAG
                           tatttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttgcaccacccctaaaagagaaggaaactgcttttaaaccctttttggggtttaatacgggaagttgagtatttgatatctctgttgaatgttgtagCTCGAAAGCCTTCCTGCTATGATTGGTGGAGTTTATTCGGACGATAACAACCTTCAGCTTGAGGCCACAACACAGTTCCGCAAGTTGCTTTCTATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
-ctttgca
- - - - - - - - aaaagaga
- - - - - - - - - - - - - - - ctgcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg