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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccccccttgcctatagatggttaatttgagaagaatttgggtagccgcgcgcgcggcgtgagatgaaactgacatgatcaccttgctgtttgtctttttgtctcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g45274.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G348512_T06 (Zea mays), 3'ss of exon 2
----gtaagccccccttgcctatagatggttaatttgagaagaatttgggtagccgcgcgcgcggcgtgagatgaaactgacatgatcaccttgctgtttgtctttttgtctcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
    || || ||||||   || |  |     |  | |       ||| | |     | |  |  || ||   |    |||  ||  | |     | ||| | |||||         |||||||||||||||||||| |||||||| ||||||||||||||||| ||||||
gtaagtcagtccccctcctctctgtacccagagctagctgctggtttcgat-----cccatggcgcttgctttctttctggaattctgagtgccccgttggccttttc-------tcgcagCAAGAAGCCGGAGCTGTTCGAGCCTCTCAAGGCCGGCCAGGCCCCCAAG

upper sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G121878_T06 (Zea mays), 3'ss of exon 3
gtaagccccccttgcctatagatggtta----atttgagaagaatttgggtagccgcgcgcgcgg---cgtgagatgaaactgacatgatcac--cttgctgtttgtctttttg--tctcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
||||| | ||   ||   | | |   |     |   | |     |||   |  ||      |       ||||  | |    |    ||   |  ||     | ||      ||    |  | |||||||||||||||||||| |||||||| |||||| ||||||||   |||| |
gtaagtcacctgagctgtttgttctctgcagcacccgcgtttggtttctatttccttttttgtttgtttgtgaattcagtgagctccgactccgactgatcatgtgctccgctgatctttgttcgcagCAAGAAGCCGGAGCTGTTCGAGCCTCTCAAGTCCGGCCAGAGCCCCAGG

upper sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G121878_T04 (Zea mays), 3'ss of exon 1
----------------------------------------------------------gtaagccccccttgcctatagatggttaatttgag--aagaatttgggtagccgcgcgcgcggcgtgagatgaaactgacatgatcaccttgctgtttgtctttttgtctcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
                                                          ||    ||   |    |  | | | || |||||      |||||  | ||      ||   |     | || |  |       |  || ||  || || | ||||| |    | | |||||||||||||||||| |||| ||| |||||| |||||||||| ||||||
gtaagtcacccctctactactcagagctggctgttgttttctgcagcaccggcgtttggtttagccgtttcagtttcaaacgtttcatttgtatcgggaattctgatatagcttcgactgatcctatattattcctgtgctagtacgtt--tgatt-tttttttcttcatttcacagCAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG

upper sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G094165_T05 (Zea mays), 3'ss of exon 2
--------------------------------------gtaagccccccttgcctatagatggttaatttgaga---agaatttgggtagccgcgcgcgcggcgtgagatgaaactgacatgatcaccttgctgtttgtctt-tttgtctcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
                                      | |  |||   | | |  | | |  ||  ||||       | | |    ||     ||| ||  |   |  |||  | | | |   | || |   | |  |||| ||| |||    |||||||||||||||||||| |||||||| ||||||||||| ||||| ||||||
gtaagtgctttgcttgattccccgatcgagcagttttcgcagccccatgtcgtcgtttgcttattggtttgtctcttgggaatgaattaattctgcgagctcc---aactgatcccgtcgttgcccccctttcgatcttcttctttttctttctcgcagCAAGAAGCCGGAGCTGTTCGAGCCTCTCAAGGCCGGTCAGGCCCCCAAG

upper sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G348512_T01 (Zea mays), 3'ss of exon 2
gtaagccccccttgcctatagatggttaatttgagaagaatttgggtagccgcgcgcgcggcgtgagatgaaactgacatgatc--accttgctgtttgtctttttgtctcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
           |   | ||        |   || |  ||||   | | |  | | |    |||    |   |  | || ||| |  | ||||   |  | ||      |   |  ||||||||||||||||||| |||||||| ||||||||   |||| | ||||||
----------gtaagcaattagctagaaccctgtgtggaatc--gatcgatgtgtgttatgcggatcaacgagtttacgtgaactgatcttgtgatccgcctcc----cgttttggcagCAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG

upper sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G094165_T04 (Zea mays), 3'ss of exon 2
--------------------------------------gtaagccccccttgcctatagatggttaatttgaga---agaatttgggtagccgcgcgcgcggcgtgagatgaaactgacatgatcaccttgctgtttgtctt-tttgtctcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG---------------------------------------------------
                                      | |  |||   | | |  | | |  ||  ||||       | | |    ||     ||| ||  |   |  |||  | | | |   | || |   | |  |||| ||| |||    |||||||||||||||||||| |||||||| ||||||||||| ||||| ||||||                                                   
gtaagtgctttgcttgattccccgatcgagcagttttcgcagccccatgtcgtcgtttgcttattggtttgtctcttgggaatgaattaattctgcgagctcc---aactgatcccgtcgttgcccccctttcgatcttcttctttttctttctcgcagCAAGAAGCCGGAGCTGTTCGAGCCTCTCAAGGCCGGTCAGGCCCCCAAGGTACGTGACTAGTACTACTCGCCCTGTAGCTCTCTCTCTATCGTCACCGGC

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|38471649|gb|CF955780.1|CF955780
EST:     AAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: AAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|38471231|gb|CF955362.1|CF955362
EST:     TCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGG-CGGGCAGGCACCCAAG
genomic: TCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|29615754|gb|CB620766.1|CB620766
EST:     TCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: TCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|38475997|gb|CF960130.1|CF960130
EST:     GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|11442915|gb|BF430814.1|BF430814
EST:     GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|36355243|gb|CF589207.1|CF589207
EST:     TCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: TCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|87012647|gb|CI295091.1|CI295091
EST:     GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|11442940|gb|BF430837.1|BF430837
EST:     GCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: GCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|29684733|gb|CB681008.1|CB681008
EST:     GTTCAAGACCGAGATTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: GTTCAAGACCGAG-TTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|38481454|gb|CF965543.1|CF965543
EST:     GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|11442622|gb|BF430525.1|BF430525
EST:     GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|38475550|gb|CF959683.1|CF959683
EST:     GCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAGGGGCGGCCAGGCACCCAAG
genomic: GCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|4715140|gb|AU056257.1|AU056257
EST:     GATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: GATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|29664042|gb|CB660317.1|CB660317
EST:     TCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: TCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|38473166|gb|CF957298.1|CF957298
EST:     GTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: GTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|58585665|gb|CF983973.1|CF983973
EST:     GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGA                         GAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
genomic: GTCGACCGCCTCAAGGATGGGTTCGCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
EST: gi|38482639|gb|CF966593.1|CF966593
EST:     GCCAAGTTCAAGACCGAGTTCTATGA                         CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGGCGGCCAGGCACCCAAG
genomic: GCCAAGTTCAAGACCGAGTTCTATGAgtaagccccc ... tcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagatgaaactgacatgatcaccttgctgtttgtctttttgtctcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG
         aactgac  putative branch site (score: 2)
                       ccttgctgtttgtctt  putative PPT
                                   tcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccccccttgcctatagatggttaatttgagaagaatttgggtagccgcgcgcgcggcgtgagatgaaactgacatgatcaccttgctgtttgtctttttgtctcctccgcagCAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT