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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaataaacttgtcttgtctttgtgcagtagttattggctgtattacatgggctttctggagaatgtcttttgttcatgaggctccttgagaaattacagtatagttgaagaggactggtcctagtgtaatttttactgattattcggtacacatgcttgtttttcacaccttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGAGGTGATGGCATGGTTAAGCTATGGCAGGCTAACCTGAATGGAGTTTGGC

Basic information

species Oryza sativa
transcript LOC_Os01g43250.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43250.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G057853_T01 (Zea mays), 3'ss of exon 7
gtacaataaacttgtcttgtctttgtgcagtagttattggctgtattacatgggctttctggagaatgtcttttgttcatgaggctccttgagaaattacagtatagttgaagaggactggtcctagtgtaatttttactgattattcggtacacatgcttgtttttcacaccttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGAGGTGATGGCATGGTTAAGCTATGGCAGGCTAACCTGAATGGAGTTTGGC
                                                                              |  ||||  |||      ||  | |  |     |||   |   |  | ||||   | | | || |||| |      ||| |||   ||    | || |||||||   ||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||  || ||||||||||||
--------------------------------------------------------------------------acgaacaaggc--cttagtcttttttatttgaacactagaccgcatctttttgtgtgtgtgtgattgtttatact---tgcat-cttacattctgaatctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGAGGAGATGGCATGGTTAAGCTATGGCAGGCTAATTTGGATGGAGTTTGGC

upper sequence: LOC_Os01g43250.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv02s0025g01250.t01 (Vitis vinifera), 3'ss of exon 7
gtacaataaacttgtcttgtctttgtgcagtagttattggctgtattacatgggctttctggagaatgtcttttgttcatgaggctccttgagaaattacagtatagttgaagaggactggtcctagtgtaatttttactgattattcggtacacatgcttgtttttcacaccttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGAGGTGATGGCATGGTTAAGCTATGGCAGGCTAACCTGAATGGAGTTTGGC
                                                                ||      || ||| ||| | |  ||   ||     |    |  ||| | |     ||  || || ||| |   |||||| |      || ||  |  || ||      | | |||||   |||  |||||||||||||| |||| |||||  | ||| | || ||||| ||||| ||||| | ||| |||||| ||||| ||||||| |||||||
----------------------------------------------------------------aaaagtacttattcttgatggtt-ttagtaagcatgaactcatctgatgtg---ctgtattaatg-aatatggtctgattgt------catatattcattgttg-----tgattagGTGTGGCAGATGGAATGGGACATGAGCGGAATGACCTTGGCAACTACTGGAGGAGATGGGATGGTAAGGCTGTGGCAGTCTAACTTGAATGGTGTTTGGC
















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|86526964|gb|CI167170.1|CI167170
EST:     GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAG                         GTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
genomic: GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAGgtacaataaa ... accttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
EST: gi|29658632|gb|CB654907.1|CB654907
EST:     GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAG                         GTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
genomic: GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAGgtacaataaa ... accttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
EST: gi|88214365|gb|CI214214.1|CI214214
EST:     GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAG                         GTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
genomic: GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAGgtacaataaa ... accttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
EST: gi|3763201|gb|AU029953.1|AU029953
EST:     GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAG                         GTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
genomic: GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAGgtacaataaa ... accttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
EST: gi|66922346|gb|CX109194.1|CX109194
EST:     GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAG                         GTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
genomic: GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAGgtacaataaa ... accttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
EST: gi|86253118|gb|CI058043.1|CI058043
EST:     GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAG                         GTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
genomic: GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAGgtacaataaa ... accttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
EST: gi|89181023|gb|CI045106.1|CI045106
EST:     GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAG                         GTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA
genomic: GCAGCCTGTCAACTGAGAATGTGGCTGTACTTTCTGGCCATGATGGGGAGgtacaataaa ... accttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtaatttttactgattattcggtacacatgcttgtttttcacaccttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGAGGTGATGGCATGGTTAAGCTATGGCAGGCTAACCTGAATGGAGTTTGGC
           tactgat  putative branch site (score: 2)
                                              ccttact  putative PPT
     aatttttactgattat  TA-rich tract