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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaacaatatatctcttgttttcttctttctatatttagtatagtcacagaagtagtttgtgttcccagttttctttctgagtcttgtgattttgttttgtgtttgattgttttttatttccttccacagAACGAAAGCCATATAACGCTGCATGACCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAA

Basic information

species Arabidopsis thaliana
transcript AT5G28900.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 10
----------------gttcaacaatatatct----cttgttttcttctttctatatttagtatagtcacagaa-gtagtttgtgttcccagttttctttctgagtcttgtgattttgttttgtgtttgattgttttttatttccttccacagAACGAAAGCCATATAACGCTGCATGACCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAA
                  | |   ||  || |    | |||||    |  |  |   | || ||  | |   |  | |   | |  | | |  || || | |         |   ||    ||  ||||||   | |||  ||  |||||||||||||  || |  | || || |  ||| | ||| | |  || ||||| || ||  | |||||||||||||| ||||||||||||||||||||||||||||
gtagcatcttggacagaattattgatgcattttaggcctgtttggaacagtggaatgtcagcatgttgaggaattgcaccatttaatgcaaaattcctgtgttccaaacaagtccttaaactgaatttgataaatcttttctt--ttccacagAACGAGTGCTACTTTACACTACGGGACTTAAAACGGTGTAAACTCTCAGGGAATATATTCAACATCCTATTCAATCTCAACAAATTTATGGCATTTGAAA

upper sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 10
gttcaacaatatatctcttgttttcttctttctatatttagtatagtcacagaagtagtttgtgt---tcccagttttctttctgagtcttgtgattttgtt---ttgtgtttgat-tgttttttatttccttccacagAACGAAAGCCATATAACGCTGCATGACCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAA
                                         |  || ||  ||  |    ||  |   | |  | ||  ||| | | |  | |   || |     |  | | |  |   | ||| |||       |||||| ||  | ||  |||| || |  ||  ||||   ||  || || ||||||||| | |||||||| || ||||||||||| |||||  ||||||||||||
---------------------------------------gatgaagccatggagattagatgcatattttcttgcttaatttgttactgcttttccttcggggaataatatcttttgcatctttgattctggattacagAAGGACGGTCACTTAACACTCCGGGATTTGAAGAACTGCAAACTATCTGGAAACTTTTTCAACATACTCTTTAATCTCAATAAATTCGTGGCATTTGAAA

upper sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 10
gttcaacaatatatctcttgttttcttctttctatatttagtatagtcacagaagtagtttgtgttcccagttttctttctgagtcttgtgattttgttttgtgtttgattgttttttatttccttccacagAACGAAAGCCATATAACGCTGCATGACCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAA
    ||   | |   |  | | |||| | ||   |  ||    || ||    || | | |   |    || |||   | ||   |  |||||    |||||   |   | |  |  |    ||   |  ||||| ||| | |   | || || |  ||| | ||  | |  ||  | ||||||||| ||||||| ||||| ||||| |||||||||||  | || ||||| |
--gtaagcgtttgagtagtctcttctacattggttgcttcac-tattcgactaaatgggtctcgcattca-tttcactgctagttaatgtgaa---gttttcactgaaacttatcctctactctggctgcagAATGAAGGACGGTTGACACTTCGGGACTTAAAGCGATGCAAATTATCTGGAAACTTCTTCAATATCCTTTTTAACCTCAACAAATTCGTAGCTTTTGAGA

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|116435329|gb|EG477921.1|EG477921
EST:     TTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAG                         AACGAAAGCCATATAACGCTGCATGACCTGAAAGGCTCAAAGCTCTCTGGA
genomic: TTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgttcaacaat ... ccttccacagAACGAAAGCCATATAACGCTGCATGACCTGAAAGGCTCAAAGCTCTCTGGA
EST: gi|116435322|gb|EG477914.1|EG477914
EST:     TTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAG                         AACGAAAGCCATATAACGCTGCATGACCTGAAAGGCTCAAAGCTCTCTGGA
genomic: TTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgttcaacaat ... ccttccacagAACGAAAGCCATATAACGCTGCATGACCTGAAAGGCTCAAAGCTCTCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgagtcttgtgattttgttttgtgtttgattgttttttatttccttccacagAACGAAAGCCATATAACGCTGCATGACCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAA
                          gtttgat  putative branch site (score: 5)
                                ttgttttttatttcct  CT-rich tract
                           tttgattgttttttat  TA-rich tract