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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctgccttgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g42320.1
intron # 1
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 1
lower sequence: GRMZM5G850355_T02 (Zea mays), 3'ss of exon 2
----------------gtatgt-gctgccttgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgt-----ggcgatttcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAG
                 ||  | |||  ||||| | || | | |   ||||||||  |   | | | |  ||| ||||    | || ||   ||||| |     |  ||||| | | ||||||||||||| ||||| |||||||| |||||||||||||| || ||||||||||| ||||| ||||| ||||||||||
gttcgtgctcccttccctacatcgctcgcttgctcgtctcccccatcgagatcggtgggatttttgcgtcgttacggtggtttgatgtgaatttttttttttcggttgattttgct-gcagCCCGTCGGGAAAGCTTGTGCAGATAGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G824831_T02 (Zea mays), 3'ss of exon 2
-----gtatgtgctgcct-tgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAG
     | || |   || |   ||||| |  || |  ||||||||| |  || | | |  ||| ||||    | ||| |   |||||  |  ||||| ||| |||| |||||||||||||| |||||||| |||||||||||||| || ||||||||||| ||||| || |||||||||||||
tccctgcatctctcgcttgctcgccttctccgtc--gagatcggggg--attttgcgtcgttacggtggtttgatccggattttttcggttgattttgtt-gcagTCCGTCGGGGAAGCTCGTGCAGATTGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCGCTCGGGATCAAAG

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G824831_T08 (Zea mays), 3'ss of exon 2
------------------gtatgtgctgcct-tgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAG
                  | || |   || |   ||||| |  || |  ||||||||| |  || | | |  ||| ||||    | ||| |   |||||  |  ||||| ||| |||| |||||||||||||| |||||||| |||||||||||||| || ||||||||||| ||||| || |||||||||||||
gttcgtgctcctctccctgcatctctcgcttgctcgccttctccgtc--gagatcggggg--attttgcgtcgttacggtggtttgatccggattttttcggttgattttgtt-gcagTCCGTCGGGGAAGCTCGTGCAGATTGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCGCTCGGGATCAAAG

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G850355_T08 (Zea mays), 3'ss of exon 1
----------------gtatgt-gctgccttgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAG
                 ||  | |||  ||| | | || | | |   ||||||||  |   | | | |  ||| ||||    | || ||   |||||  |  |||||| | |||||||||||||| ||||| |||||||| |||||||||||||| || ||||||||||| ||||| ||||| ||||||||||
gttcgtgctcccctcgctacatcgctcgcttactcgtctcccccatcgagatcggtgggatttttgcgtcgttacggtggtttgatgtgaatttttttggttgatttc-tctgcagCCCGTCGGGAAAGCTTGTGCAGATAGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G824831_T04 (Zea mays), 3'ss of exon 2
------------------gtatgtgctgcct-tgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAG
                  | || |   || |   ||||| |  || |  ||||||||| |  || | | |  ||| ||||    | ||| |   |||||  |  ||||||||| |||| |||||||||||||| |||||||| |||||||||||||| || ||||||||||| ||||| || |||||||||||||
gttcgtgctcctctccctgcatctctcgcttgctcgccttctccgtc--gagatcggggg--attttgcgtcgttacggtggtttgatccggattttttcggttgatttcgtt-gcagTCCGTCGGGGAAGCTCGTGCAGATTGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCGCTCGGGATCAAAG

upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G850355_T01 (Zea mays), 3'ss of exon 2
-gtatgt-gctgccttgcgcctccctcgcccggagatcgggcgtgatctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAG
  ||  | |||  ||| | | || | | |   ||||||||  |   | | | |  ||| ||||    | || ||   |||||  |  |||||| | |||||||||||||| ||||| |||||||| |||||||||||||| || ||||||||||| ||||| ||||| ||||||||||
gctacatcgctcgcttactcgtctcccccatcgagatcggtgggatttttgcgtcgttacggtggtttgatgtgaatttttttggttgatttc-tctgcagCCCGTCGGGAAAGCTTGTGCAGATAGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG

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|88590186|gb|CI709019.1|CI709019
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
EST: gi|88759914|gb|CI769470.1|CI769470
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
EST: gi|87011186|gb|CI287863.1|CI287863
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
EST: gi|86847609|gb|CI288727.1|CI288727
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
EST: gi|88391828|gb|CI603347.1|CI603347
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCCGGTCGGAT
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGC-GGTCGGAT
EST: gi|88745867|gb|CI769227.1|CI769227
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGNGGTCGGATT
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
EST: gi|88294492|gb|CI667466.1|CI667466
EST:     TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAG                         CCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC
genomic: TCGGCGGCCATGGGAGACAGCCAGTACTCCTTCTCCCTCACCACCTTCAGgtatgtgctg ... tcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctggtgcggtttcggtttcgtcatctgtggtttttgtggcgatttcgtttgcagCCCGTCGGGGAAGCTGGTGCAGATCGAGCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAG
                                           tttcgttt  CT-rich tract
                               tttttgt  TA-rich tract