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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagttatctttgagtgttctcaaagttagaattttgttatcctcatatgtccaaaaccttgctaacattatggatataccttttaacttgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTGCACGGTAGCAACAAGAAGTTCGATACTGATGTCTCTCTTGAAGTCATAG

Basic information

species Oryza sativa
transcript LOC_Os06g45820.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 2
---ttgagttatctttgagtgttctcaaagttagaattttgttatcctcatatgtccaaaaccttgct-aacattatggatataccttttaacttgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTGCACGGTAGCAACAAGAAGTTCGATACTGATGTCTCTCTTGAAGTCATAG
   ||  |||    ||||    |||  |      |      | |  || ||  |          | || || ||  ||  ||| ||||  || | |||||||||||   ||||||||||||||||||||| ||||||||||||||||| || ||||| ||| |||||||||| || ||| ||||||| ||||| || |||||||
ccatttggttcagcttgatccatctttattccgta----cctgacactaattcgctgggggttgtccttaatatcttgagtatgccttaaaattcgttgcacagGTGTCTGTTGATGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTGCATGGTGGCAACAAGAAATTTGATTCTGATGTTTCTCTCGATGTCATAG

upper sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G087598_T03 (Zea mays), 3'ss of exon 2
ttgagttatctttgagtgttctcaaagttagaattttgttatcctcatatgtccaaaaccttgctaacattatggatataccttttaacttgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTGCACGGTAGCAACAAGAAGTTCGATACTGATGTCTCTCTTGAAGTCATAG-----------------------------------------------------------------------------
                                                                                                           | || |||||||||||||| ||||||||||||||||| || ||||| |||||||||||||| || ||| ||||||| |||||||| |||||||                                                                             
-----------------------------------------------------------------------------------------------------------tcgacgttcctgatgtacgtggaaggacagagattctaaaagtgcatggtagcaacaagaaatttgattctgatgtttctcttgatgtcatagcaatgagAACACCTGGGTTCAGCGGAGCAGACTTGGCAAACCTTCTGAATGAAGCAGCCATTCTGGCTGGAAGACGG

upper sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G087598_T01 (Zea mays), 3'ss of exon 2
ttgagttatctttgagtgttctcaaagttagaattttgttatcctcatatgtccaaaaccttgctaacattatggatataccttttaacttgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTGCACGGTAGCAACAAGAAGTTCGATACTGATGTCTCTCTTGAAGTCATAG
|| |  | || || | |      | | |    |  |  | |     |||| |        ||  ||||||  | | ||| |||| ||| |  || |||||||   ||| || |||||||||||||| ||||||||||||||||| || ||||| |||||||||||||| || ||| ||||||| |||||||| |||||||
ttcatctttcattcaatacctgaacactagttagatcttaacggaaatatatgggggttgttcttaacatctttggtatgccttgtaattcattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTGCATGGTAGCAACAAGAAATTTGATTCTGATGTTTCTCTTGATGTCATAG

upper sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 2
ttgagttatctttgagtgttctcaaagttagaattttgttatcctcatatgtccaaaaccttgctaacattatggatataccttttaacttgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTGCACGGTAGCAACAAGAAGTTCGATACTGATGTCTCTCTTGAAGTCATAG
               || |  | | | |  ||| |   | || ||  | ||    |        ||| ||||    || || |  |  ||| ||   ||||| |  ||||||||||| ||| || | |||||||| || || || ||||| || | ||||||||| ||||| ||| ||||||| ||||||||||| || |
---------------gtatgattatattatgaaatgcctcatgcttttgtgaatgag-------taa-attac---taaacatcattgcttttt---cagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG

upper sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G09160.1 (Glycine max), 3'ss of exon 2
ttgagttatctttgagtgttctcaaagtta-gaattttgttatcctcatatgtccaaaaccttgctaacattatggatataccttttaacttgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTGCACGGTAGCAACAAGAAGTTCGATACTGATGTCTCTCTTGAAGTCATAG
               || ||    | |||| ||| |   | || ||  | |    ||    |   | ||   |   | | | | |  |   | ||||  |||| |  ||||||||||| ||| || | |||||||| || || || ||||| || | ||||||||| ||||| ||| ||||||| ||||||||||| || |
---------------gtattgattatgttatgaaatgcctaatgcttttgt---taatgattaaattactgaacaaaaaaaacatcaatgcttttgc--agGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG

upper sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 3'ss of exon 2
ttgagttatctttgagtgttctcaaagttagaattttgttatcctcatatgtccaaaaccttgctaacattatggatataccttttaacttgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTGCACGGTAGCAACAAGAAGTTCGATACTGATGTCTCTCTTGAAGTCATAG
                 ||   || ||  |  || ||||| |   | | | ||    |  ||   |     |   |  ||| ||  | ||| | |  ||||||| |||||||||||||||| |||| ||||||||||||||  | ||||| || | | | || |||||||| |||   ||||| |||||||| || ||||
-----------------gtaagcatagagaatatattgttttttgcct-tatctttta--ttataagtgggaaatacttacgttaaagctt-tggagcagGTAACTGTTGATGTTCCTGATATACGGGGAAGGACAGAGATCTTAAAGGTTCATGCTGGTAATAAGAAGTTTGATGGAGATGTGTCTCTTGATGTAATAG

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|2798681|gb|AA751975.1|AA751975
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|58692405|gb|CK081092.1|CK081092
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|58681961|gb|CK070648.1|CK070648
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|58607022|gb|CK035055.1|CK035055
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|2428427|gb|C72890.1|C72890
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|313079833|gb|HO213272.1|HO213272
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGAT
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGAT
EST: gi|58693754|gb|CK082441.1|CK082441
EST:     GTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|58608816|gb|CK036849.1|CK036849
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|25797955|gb|CA753916.1|CA753916
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|58693479|gb|CK082166.1|CK082166
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgtccaaaaccttgctaacattatggatataccttttaacttgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTGCACGGTAGCAACAAGAAGTTCGATACTGATGTCTCTCTTGAAGTCATAG
                   taacattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagttatctttgagtgttctcaaagttagaattttgttatcctcatatgtccaaaaccttgctaacattatggatataccttttaacttgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTGCACGGTAGCAACAAGAAGTTCGATACTGATGTCTCTCTTGAAGTCATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG