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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctaacatcactcttaatgctgaattcctcttttagtgagttgcgacatgctattcgttgtttgtttctcagaagcactaatacatagttatatgcaaattcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG

Basic information

species Oryza sativa
transcript LOC_Os02g42320.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G850355_T02 (Zea mays), 3'ss of exon 4
gtaagtctaacatcactcttaatgctgaattcctcttttagtgagttgcgacatgctattcgttgtttgtttctcagaagcactaa-tacatagttatatgcaaa---ttcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
||| || || | | | | ||     ||||||  |  | ||      ||| |||| ||   |    ||| | | | | |||  ||||  | |||  |  ||| |||   |||||||||||||||||||| || | || || || |||||||||||||| ||
gtatgtgtacc-taagtttt-----tgaatt--ttctcta------tgccacattcttacc----tttctctatgataagtgctaaacagatacctgcatgaaaacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G850355_T03 (Zea mays), 3'ss of exon 3
gtaagtctaacatcactcttaatgc-tgaattcctcttttagtgagttgcgacatgctattcgttgtttgtttctcagaagcactaa-tacatagttatatgcaaa---ttcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
          ||||  | |   | | | | ||  |   ||       ||| |||| ||  ||    ||| | | | | |||  ||||  | |||  |  ||| |||   |||||||||||||||||||| || | || || || |||||||||||||| ||
----------catctgtatgtgtacctaagtttttgaattttctctatgccacattcttatc----tttctctatgataagtgctaaacagatacctgcatgaaaacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 4
gtaagtctaacatcactcttaatgctgaattcctcttttagtgagttgcgacatgctattcgttgtttgtttctcagaagcactaa-tacatagttatatgcaaa----ttcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
||| || || | | | | ||     |||||| |||||||        || |||| ||   |    ||| |   | |  ||  ||||  | |||  |  ||| |||    |||||||||||||||||||| || | || || || |||||||||||||| ||
gtatgtgtatc-taagtttt-----tgaatttctctttt--------gccacattctgacc----tttctccatgacgagtgctaaacagatacctgcatgaaaaacttttcagGTGCAAAAGATTCAGGCACTAACACCTAATATTGGAGTTGTCTATAG

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G850355_T08 (Zea mays), 3'ss of exon 3
gtaagtctaacatcactcttaatgctgaattcctcttttagtgagttgcgacatgctattcgttgtttgtttctcagaagcactaa-tacatagttatatgcaaa---ttcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
||| || || | | | | ||     ||||||  |  | ||      ||| |||| ||  ||    ||| | | | | |||  ||||  | |||  |  ||| |||   |||||||||||||||||||| || | || || || |||||||||||||| ||
gtatgtgtacc-taagtttt-----tgaatt--ttctcta------tgccacattcttatc----tttctctatgataagtgctaaacagatacctgcatgaaaacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S2_595V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------gtaagtctaacatcact-cttaat----gctgaattcctctttta--gtgagttgcgacat---gctattcgttgtttgtttctcagaagcactaatacatagttata--------tgcaaattcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
                                                                 | | |  |  ||    | ||| ||      ||| ||| |   |||   | || | |  | |     |||| | |      |  ||| |      ||||  |  | ||         |  |   |||| |  | || |||||||||||||| || ||||| ||||||||||||||
gtgagttatctttcgcaagtttttattttatgcgaaactagggttttgtatgctgctgaacttccgcacggttgccacggtttcttgatcgccagtgatttcttgcattaccataaggtacagcttcgaaatatttgcttcagcgtattcaaatttgtgaatagttgctgatgatatcctctttattctcagATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG

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|56550165|gb|CX056269.1|CX056269
EST:     TGCCTTCTATTTTAGTCGATGAAACATCT                         GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
genomic: TGCCTTCTATTTTAGTCGATGAAACATCTgtaagtctaa ... gcaaattcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
EST: gi|27554138|gb|CA998038.1|CA998038
EST:     GAAATTGCCTTCTATTTTAGTCGATGAAACATCT                         GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
genomic: GAAATTGCCTTCTATTTTAGTCGATGAAACATCTgtaagtctaa ... gcaaattcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
EST: gi|27578244|gb|CB000939.1|CB000939
EST:     TTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT                         GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
genomic: TTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCTgtaagtctaa ... gcaaattcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
EST: gi|88288359|gb|CI661564.1|CI661564
EST:     TTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT                         GTGCAAAAGATTC
genomic: TTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCTgtaagtctaa ... gcaaattcagGTGCAAAAGATTC
EST: gi|27576119|gb|CA998813.1|CA998813
EST:     TGCCTTCTATTTTAGTCGATGAAACATCT                         GTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
genomic: TGCCTTCTATTTTAGTCGATGAAACATCTgtaagtctaa ... gcaaattcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctattcgttgtttgtttctcagaagcactaatacatagttatatgcaaattcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG
                          cactaat  putative branch site (score: 2)
                             taatacatagttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctaacatcactcttaatgctgaattcctcttttagtgagttgcgacatgctattcgttgtttgtttctcagaagcactaatacatagttatatgcaaattcagGTGCAAAAGATTCAGTCATTGACTCCGAACATTGGAGTTGTCTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG