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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatttctacatgttgaatcatagggtgactaatgtagattgcatgttacttttcttctgttaatttgtcacaaatttcttaaacggaatcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCGATTCCGCATCCAACGGACCCAGCTCAGGCAGCGAATCAAGGTCAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os06g13820.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 21
catatttctacatgttgaatc-atagggtgactaatgtagattgcatgttacttttcttctgtt---aatttgtcacaaatttcttaaacggaatcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCGATTCCGCATCCAACGGACCCAGCTCAGGCAGCGAATCAAGGTCAAGAAG
 |||||| | ||  |||     ||   |||   |  | || | |  |  |  |||     | |    ||  | ||  |||  ||   ||    || ||||||||||||||| || ||||| | |||| |||||||||| |||||||| || || |||||||| || || || ||     | || |||  |   ||   |  |||
tatattt-tgcaaattggtcggatgcagtgcacacggaaggtagatttctgttttcaccttatgcggaacatttcgtaaagatc---aaatttattatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTGATTCCGCTTCAAATGGTCCTGTTGCTGGAAGCACAAACAGTCAATCAAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 9
catatttctacatgttgaatcatagggtgactaatgtagattg-catgttacttttct--tctgt-taatttgtcacaaatttcttaaacggaatcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCGATTCCGCATCCAACGGACCCAGCTCAGGCAGCGAATCAAGGTCAAGAAG
     ||  ||    | ||||   |   ||   |  | ||||| |||   |     |    || | |      |  |  |   || |||    || ||||||||||||||| || ||||| | |||| |||||||||| |||||||||||||| |||||  | || || || ||     |    |||  |   ||   |  |||
--ggatttaactcacttaatccc-gtccgatccacatggattgacatcgaaacagacagacctatgtggaacatttcgtaacgctcaaa-attattatttgcagAGAGCCCTCGAACACCAAGCCGCTCAGGTGAGGACTGGAGGTCTGCCTTTGATTCATCTTCAAATGGGCCTGTTGCTACAAGCACAAACAGTGAATCAAG
















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|29625476|gb|CB630487.1|CB630487
EST:     GGTCCATGACAACAGGGCTGCTTCTTATGCCAAGGATATCTCTGAAGTTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|89190153|gb|CI392203.1|CI392203
EST:     TGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGA-GTCTGCCTTCG
genomic: TGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|29662868|gb|CB659143.1|CB659143
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|27921374|gb|CB097182.1|CB097182
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|88221475|gb|CI221431.1|CI221431
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|29614012|gb|CB619025.1|CB619025
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|87023303|gb|CI272131.1|CI272131
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|87027749|gb|CI274313.1|CI274313
EST:     TCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|87015008|gb|CI273406.1|CI273406
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTC
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCC-GGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTC
EST: gi|86430557|gb|CI082980.1|CI082980
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|86482222|gb|CI124855.1|CI124855
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|88198327|gb|CI198177.1|CI198177
EST:     CTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: CTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|86430146|gb|CI082569.1|CI082569
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|29625430|gb|CB630441.1|CB630441
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|218497504|gb|FG955306.1|FG955306
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|88841689|gb|CI080945.1|CI080945
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|29622848|gb|CB627859.1|CB627859
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|88532772|gb|CI461403.1|CI461403
EST:     CTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: CTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|86482007|gb|CI124640.1|CI124640
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|25798429|gb|CA754390.1|CA754390
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCNATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|88197116|gb|CI196966.1|CI196966
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCCATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|66912617|gb|CX099465.1|CX099465
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|87040350|gb|CI194972.1|CI194972
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|86827768|gb|CI272958.1|CI272958
EST:     GCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
genomic: GCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG
EST: gi|86898985|gb|CI296187.1|CI296187
EST:     TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTG                         AGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATCGGAGGTCTGCCTTCG
genomic: TGTCCATGACAACAGGGCTGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttac ... tcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttacttttcttctgttaatttgtcacaaatttcttaaacggaatcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCGATTCCGCATCCAACGGACCCAGCTCAGGCAGCGAATCAAGGTCAAGAAG
              tgttaat  putative branch site (score: 3)
                          acaaatttcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatttctacatgttgaatcatagggtgactaatgtagattgcatgttacttttcttctgttaatttgtcacaaatttcttaaacggaatcatttgcagAGAGCCCCCGGACACCCAACCGCCCAGGTGAGGATTGGAGGTCTGCCTTCGATTCCGCATCCAACGGACCCAGCTCAGGCAGCGAATCAAGGTCAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG