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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattcttcttatctatgctgctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC

Basic information

species Oryza sativa
transcript LOC_Os04g56970.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
----gtaagtattcttcttatctatgctg------ctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
    ||   |  ||  |||  ||   ||       ||| || |||| ||||   |   || ||  |  ||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||||||||
gtgggtggtttctcccctttcctgctctaacttatctgcaaattgttatcatgta--ccttatgagtgaacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 5
-------------------------------gtaagtattcttcttatctatgctgctgt-aacttgtgatcacacaatactcatctgaaaacttt-gcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                                 || || |       |  ||  || ||| | ||| |||  | |  ||   |   || |   |||  |||||||| || ||||| ||||| |||||||||||||| |||||||| |||||| ||||||||||||| ||||||||||| |||||||| ||||| ||||| |
tatttgagtgttgctcctccaccataattggacaattaatgaaaa-gtacattttgatgtcagcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 5
--------------------------------------gtaagtattcttcttatctatgctgctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                                      ||||      || | || |  |||  |  |   ||| ||       |||   |||      ||| ||||||||||| ||||| ||||| |||||||||||||| |||||||| |||||| ||||||||||||||||||||||||| |||||||| ||||| ||||| |
tttcagtgttgctcctccatcataattggacaattaatgtaaagtacattttgatgtcagcttat-caggatgttattcagtgttacgtgtct-----ttttacagATACCTGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCAATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 4
---------------------------gtaagtattcttcttatctatgctgctgtaacttgtgatc----acacaatactcatctgaaaact-ttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                            |  | |||| | | |    |    |  |   || |  |     |||  |||  |   ||     | |||||| ||||||||||||||||||| |||||||| ||||| |||||||| |||||| ||||||| |||||||||||||| || |||||||| ||| | ||||| |
tcacttcttcataattgggcattttggctttgcattcatgtcaagggtatgtccatgctttttttttctcgacattataaactgttgtgccttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 4
----------------------------gtaagtattcttcttatctatgctgctgtaacttgtgatcacacaatactcatctgaaaa----ctttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                             |  | |||  | | |    |    |  |   || |  || ||  | | | | |||          |||||| ||||||||||||||||||| |||||||||||||| |||||||| |||||| ||||||| ||||||||||||||||| |||||||| ||| | ||||| |
acttctccttcataattgggcattgtggctttgcatttatgtcaagggtatgtccatggatttttttctcaacacagtaaactggtgtgccttcttgcagGTACCTGGACTTGTCAATGTAGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGTGTAGGTGTTTCATCCGGTAAAAACC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------gtaagtattcttcttatctatgctgctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                                         | | || ||| ||   |      |   |  || |||  | ||| ||   || |      ||| |||||||||||||| |||||||| |||||||| |||||||| || || |||||| | ||||||||||||||||| || || |||||||||||||||||||| |
gtgagtctatgtattgtataaagcacataacaagttggttgatgaatgcttattgattg-atccccaaagattctgaggaaacagtatatattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC

upper sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------gtaagtattctt-cttatctatgctgctgtaact-tgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
                                   | || |     |||||| ||||| ||   || | | ||   | ||||  | | |      |||||||||||| || || || |||||||||||||| ||||| || || || |||||  |||||||||||||||||||||| || || ||||||||||||||||| |
actgatttattatgatattttcctgattaatttccaatactgaagtttatctttgctgttgatcctatataatt-taaaatag-cgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC

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|29655620|gb|CB651895.1|CB651895
EST:     CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCACATATTATTACA                         ATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGACA
genomic: CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACAgtaagtattc ... aactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA
EST: gi|2311708|gb|C27863.1|C27863
EST:     GGAATATCAGATATTATTACA                         ATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA
genomic: GGAATATCAGATATTATTACAgtaagtattc ... aactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA
EST: gi|29655649|gb|CB651924.1|CB651924
EST:     CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACA                         ATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAGAGCTGTTATGAAA
genomic: CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACAgtaagtattc ... aactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA
EST: gi|29655650|gb|CB651925.1|CB651925
EST:     CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACA                         ATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA
genomic: CAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACAgtaagtattc ... aactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctatgctgctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC
            ctgtaac  putative branch site (score: 3)
                                           aaaacttt  TA-rich tract