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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCAGAGGGCCGAGCCAGTAATTATGGATGAGAGCATGATGAAGGCTTGTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaataatgtttctccagcctcttccattaaacattaactcttcttatatcttgatgctgatacggtttttgtttttgttctattaccag

Basic information

species Oryza sativa
transcript LOC_Os01g61500.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g61500.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G014720_T01 (Zea mays), 5'ss of exon 2
AGAGCAGAGGGCCGAGCCAGTAATTATGGATGAGAGCATGATGAAGGCTTGTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaataatgtttctccagcctcttccattaaacattaactcttcttatatcttgatgctgatacggtttttgtttttgttctattaccag
|||||||| ||  ||||| || ||||||||||| |||||||||||||| |||| ||||||||  ||||| |||| ||||||||| |  || ||||| |||||||||| | | |   ||| |  | || |   ||     ||||   ||| | |  |       |  |     |  || | ||  | | |      
AGAGCAGAAGGTTGAGCCTGTGATTATGGATGAAAGCATGATGAAGGCATGTGCGGCTGTTGCTCGTGTTAGAGTTGAAGTTGATAAGCTGTCTGCTAAGgtgaagggacattccatctgc--cttccttagttgt---ttaagcattcatgtgccaaagcatttctggtactcatgctgttcctttgtag----

upper sequence: LOC_Os01g61500.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G046418_T01 (Zea mays), 5'ss of exon 2
AGAGCAGAGGGCCGAGCCAGTAATTATGGATGAGAGCATGATGAAGGCTTGTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaataatgtttctccagcctcttccatt-aaacattaac---tcttcttatatcttgatgctgatacggttt---ttgtttttgttctattaccag-----------------
|||||||| ||  ||||| || ||||||||||||||| |||||||||| |||||||||||||  ||||| |||||||||||||| || || ||||| |||||||||||| | |   |||||  |||  |   || ||  ||  |    || | |||| ||||| |||| || | | ||   |||||||| |||    |  |                  
AGAGCAGAAGGTTGAGCCTGTGATTATGGATGAGAGCGTGATGAAGGCATGTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaacattccatctccttccttatttgtttaagaatccatgtgtcatattatttcttg-tgctcatgctgcttcctttgttttttttcctaaatgaatgttgtttcttttgtag
















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|86415279|gb|CI069682.1|CI069682
EST:     GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
genomic: GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
EST: gi|86542293|gb|CI182499.1|CI182499
EST:     GTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
genomic: GTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
EST: gi|86504097|gb|CI146730.1|CI146730
EST:     GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
genomic: GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
EST: gi|86599345|gb|CI251303.1|CI251303
EST:     GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
genomic: GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
EST: gi|88963710|gb|CI029483.1|CI029483
EST:     GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
genomic: GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
EST: gi|86420400|gb|CI056389.1|CI056389
EST:     GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
genomic: GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
EST: gi|218486310|gb|FG947933.1|FG947933
EST:     GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGGTTGAGGATAAA
genomic: GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
EST: gi|86835390|gb|CI347847.1|CI347847
EST:     GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
genomic: GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
EST: gi|58685366|gb|CK074053.1|CK074053
EST:     GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGGTTGAGGATAAA
genomic: GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
EST: gi|218494744|gb|FG957721.1|FG957721
EST:     GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGGTTGAGGATAAA
genomic: GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA
EST: gi|55410181|gb|CV722557.1|CV722557
EST:     GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGG
genomic: GTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGG
EST: gi|86842371|gb|CI335269.1|CI335269
EST:     TGGCCGTGTAAGAGCTGAAGTTGACACACTCTCTGCCAAG                         GTATGTGATTTGGAGAAGAGTGTGTTTCCAGGGAGAAAGATTGAGGATAAA
genomic: TGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaat ... ctattaccagGTATGTGATTTGGAGAAGAGTGTGTTTGCAGGGAGAAAGATTGAGGATAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCAGAGGGCCGAGCCAGTAATTATGGATGAGAGCATGATGAAGGCTTGTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaataatgtttctccagcctcttccattaaacattaactcttcttatatcttgatgctgatacggtttttgtttttgttctattaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG