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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctagcctttccttcccaattatattctctaaatttgatttgccatttcactgaatagtgtatttctgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTGTCTTCCGATTGGGAAGGCTAAG

Basic information

species Oryza sativa
transcript LOC_Os08g42410.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 8
gtatgcta-gcctttcctt-cccaattatattctctaaatt-------tgatttgccatttcactgaatagtgtattt--ctgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTGTCTTCCGATTGGGAAGGCTAAG
|||||  | | |||||  | | ||| |||||||||||  ||       ||| ||| ||| ||| |  ||| || ||||  |||||| |||||||||||||| ||||| ||||| || || ||||||||||||||||| ||||||||||| |||||||||
gtatgaaatgtctttctgtgctcaactatattctctatgttgtttgtttgaattgacatctcattatataatgcattttcctgcagTTATGGTGAATCATTTCCTGTATCTGCTGAGGTACTTGATTCTAGCTTCTGCCTTCCGATTGGAAAGGCTAAG

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA14G02380.2 (Glycine max), 3'ss of exon 8
-----------------------------------------------------------gtatgctagcctttccttcccaattatattctctaaatttgatttgc----catttcactgaatagtgtat-ttctgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTGTCTTCCGATTGGGAAGGCTAAG
                                                             |||  |     |  |     ||| |    ||     ||| ||        |||| | |  || |  ||| | ||  || |||||||| |||||||||||||| || |||||||||||||| || || || ||||| || || || || |||
gtaagttgtgctgcttgattctcccaccccaaaaaagacacttgtgctgcttgatttgtacatgaaaatgagtggtcatagattttgacatcagttcttgtttcaaaaaatatttaatttgatggattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 8
-----------------------------------gtatgctagcctttccttcccaattatattctctaaatttgatttgccatttcactgaatagtgtatttctgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTGTCTTCCGATTGGGAAGGCTAAG
                                   |||  |     |||      || || |  | || |||| | ||||   |||||| |||||  |||    ||  || |||||||| |||||||||||||| || |||||||||||||| || || || ||||| || || || || |||
gtaagttgtgctgcttggtttgttcatgaaaatgagtagtcatagattttgacatcagttcttgtttcaaaatat-attta--atttca-tgaattatgt---cctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 8
-----------------------------------------------------------gtatgctagcctttccttcccaattatattctctaaatttgatttgc----catttcactgaatagtgtat-ttctgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTGTCTTCCGATTGGGAAGGCTAAG
                                                             |||  |     |  |     ||| |    ||     ||| ||        |||| | |  ||    ||| | ||  || |||||||| |||||||||||||| || |||||||||||||| || || || ||||| || || || || |||
gtaagttgtgctgcttgattctcccgccccaaaaaagactcttttgctgcttgatttgtacatgaaaatgagtagtcatagattttggcatcagttcttgtttcaaaaaatatttaatttgatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------gtatgctagcctttccttcccaattatattctctaaatttgatttgccatttcactgaatagtgtatttc-tgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTGTCTTCCGATTGGGAAGGCTAAG
              ||   |    | |        |||| |  ||      |    |    |  ||  | ||| |  |   || ||||| |||||||||||||||||| |||| |  ||||  |||||||| || ||||||||||| || || || || |||
gtaagtagtattcctaatttgagttcttgcatgtgattagagcctacggtctcatatcagtacctccttaaattgatttcatcatgcagATATGGTGAATCATTCCCTATTTCAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAG

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|33824375|gb|CF338004.1|CF338004
EST:     GCAGCAATCAGGGATCCAGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTG
genomic: GCAGCAATCAGGGATCCAGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatgctagc ... atttctgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTG
EST: gi|38472326|gb|CF956457.1|CF956457
EST:     GCAGCAATCAGGGATCCAGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTG
genomic: GCAGCAATCAGGGATCCAGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatgctagc ... atttctgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTG
EST: gi|218484233|gb|FG953202.1|FG953202
EST:     GCAGCAATCAGGGATCCAGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTG
genomic: GCAGCAATCAGGGATCCAGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatgctagc ... atttctgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattatattctctaaatttgatttgccatttcactgaatagtgtatttctgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTGTCTTCCGATTGGGAAGGCTAAG
                                            tatttct  CT-rich tract
     atattctctaaattt  TA-rich tract