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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagcaaattcattttctattgacgatttcagtcattgccaaagcttatatatatatcttacggtttcttatgtggttgcagCAAGTGTATGATTATGATACATTTTCTGCTGATGACATAATGGGAGAAGCAGATATTGATATACAACCTTTGATAACATCTGCAATGGCTTTTGGGGATC

Basic information

species Arabidopsis thaliana
transcript AT4G05330.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G13700.1 (Glycine max), 3'ss of exon 8
---------------gtaagagcaaattcattttctattgacgatttcagtcattgccaaagcttatatatatatcttacggtttcttatgtg-gttgcagCAAGTGTATGATTATGATACATTTTCTGCTGATGACATAATGGGAGAAGCAGATATTGATATACAACCTTTGATAACATCTGCAATGGCTTTTGGGGATC
               ||  | |    | |||     |      |  | | |  | |    ||  |||  | |  || |    |   || | || | ||||| |||| | |||| |||| ||||||||||||||||| ||||||||||||||||| |||||| | ||  || ||||||||||||| ||||| ||||| ||| 
ttccctattctctctgtgtgtgtctgtacatgggaaagaagataactgatttttggtttgagaatatg-acacttcatcttatcaattgtctgtgctgcagAAAGTATTTGATCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG

upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 8
-------------gtaagagcaaattcattttctattgacgatttcagtcattgccaaagcttatatat-atatcttacggtttcttatgtg-gttgcagCAAGTGTATGATTATGATACATTTTCTGCTGATGACATAATGGGAGAAGCAGATATTGATATACAACCTTTGATAACATCTGCAATGGCTTTTGGGGATC
             ||  | |    ||  |         |  |  | | | ||||           |||| | |  | | | | ||   |||  ||||||| |||| | |||  |||| ||||||||||||||||| ||||||||||||||||| |||||| | ||  || ||||||||||||| ||||| ||||| ||| 
aatgcatctcgctgtgtgtgtgtgtttgtacatgggaaagaagataactgattgttggtttgagaatatgacacttcatgttatcaattgtctgttgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG

upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 6
-----------------gtaagagcaaattcattttctattgacgatttcagtcattgccaaagcttatatatatatcttacggtttcttatgtggttgcagCAAGTGTATGATTATGATACATTTTCTGCTGATGACATAATGGGAGAAGCAGATATTGATATACAACCTTTGATAACATCTGCAATGGCTTTTGGGGATC
                 |  | || | || ||      |||   | | | |   |     |||  ||||    ||   ||        | ||    |||||| | || | |||||||||    ||||| ||||||||||||||||| ||||||||||||||| | || ||  |||||||||| ||||| || |  || ||| 
ttgtctctctgtgtttggatacagaagatacaaaactaatttctggtgtaaa--aacatgaaactttattctaatggtttggttacattaattgcattgcagAATGTATTTGATTATGACTTGTTTTCGGCTGATGACATAATGGGGGAAGCAGATATTGATCTTCAGCCGCTGATAACATCCGCAATAGCATACGGAGATG

upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------------------------------------------------------gtaagagcaaattcattttctattgacgatttcagtcat---tgccaaagcttatatatatatctta-cggtttcttatgtgg--ttgcagCAAGTGTATGATTATGATACATTTTCTGCTGATGACATAATGGGAGAAGCAGATATTGATATACAACCTTTGATAACATCTGCAATGGCTTTTGGGGATC
                                                                                                           ||| | |    ||  |     |   || |  |   |      ||  ||| | | ||  | |||| || | | |  |||  | |  |||||| | || | |||||||||    ||||| ||||||||||||||||| ||||||||||||||| | || ||  |||||||||| ||||| || |  || ||| 
gtaagattgaatttcatcttgtattgttagaaaatggaaacaaattctgtgatgcttattcggtgtttggatatttggatcttcatgtgtgatacttctatttgtctgtatgtgtgttttggtacagaagatacaaaattgatttctggtgtaaaaacatgtaattttatcctaactgctggttacattgcattgcagAATGTATTTGATTATGACTTGTTTTCGGCTGATGACATAATGGGGGAAGCAGATATTGATCTTCAGCCCCTGATAACATCCGCAATCGCATACGGTGATG

upper sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 8
-------------gtaagagcaaattca-ttttctattgacgatttcagtcattgccaaagcttatatata-tatcttacggtttcttatgtggttgcagCAAGTGTATGATTATGATACATTTTCTGCTGATGACATAATGGGAGAAGCAGATATTGATATACAACCTTTGATAACATCTGCAATGGCTTTTGGGGATC
              | | |  ||||  | ||  | ||   ||||  || |  || |   |  ||  || || ||| | |    |   | |     ||||| |||| | |||  |||| || || |||||||||||||||||||||||||| || ||||| || |||||  |||||||||| || ||||| |||||  || 
cctttcatcattattcataaaaaatcaaattccccatgctcgatcacaatgttttcatgacatttcatctaatatatgagtcctgtctctcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATG

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|125187616|gb|EL202570.1|EL202570
EST:     ATCAAGAACTCATGCTGTCTGTTCCTGAGAGCTATGGCCCTGTGAAATTG                         CAAGTGTATGATTA
genomic: ATCAAGAACTCATGCTGTCTGTTCCTGAGAGCTATGGCCCTGTGAAATTGgtaagagcaa ... gtggttgcagCAAGTGTATGATTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtcattgccaaagcttatatatatatcttacggtttcttatgtggttgcagCAAGTGTATGATTATGATACATTTTCTGCTGATGACATAATGGGAGAAGCAGATATTGATATACAACCTTTGATAACATCTGCAATGGCTTTTGGGGATC
                            atcttac  putative branch site (score: 3)
             aaagcttatatatata  TA-rich tract