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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcctttttcttctgcaagatttgtttcgaaaaaatgttatgtgctgtaacgcactcttgcaaaatgttactttcagCATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAG

Basic information

species Arabidopsis thaliana
transcript AT1G17720.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 2
gtgagttcctttttcttctgcaagatttgtttcgaaaaaatgttatgtgctgtaa-cgcactcttgcaaaatgttactttcagCATGGAGGGTCCA--GGAAGGATCTTGAGCAGACGGATTACCCAGTT---AGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAG
|| ||| |   |    | |  ||| | | |        ||| ||   ||||  || | |       || | || || | |  |    ||  |      |    || ||||||  |   || || |  |||   |||||||||||||| || || || || |||||||||||||||||||| |||
gtaagtgc---tacactatataagttctat--------aatctttcttgcttaaatctcgtgtgcccatagtgctaatgtatgtgcagAATGCTTGTCGAGGAGAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 2
--gtgagttcctttttcttctgcaagatttgtttcg-----aaaaaatgttatgtg------ctgtaacgcactc----ttgcaaaatgt-tactttc----------agCATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGT---TAGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAG
    || |   |||| ||| ||||||  || ||  |     ||||||    |  |        ||| | |||||     ||| || |||| |  ||||          ||||||| || || || | |||| | |||  || ||| ||  |  |   ||||||||||||||| || || |||||||| |||||||||||||| ||||||
gtaagactattttttgcttatgcaagtgtttttgtgtaaaaaaaaaaaaccaaataggttccttgttatgcacttaatattgtaacatgtatgttttctgaaacatgcagCATGGTGGATCAAGAAGGGATTTGGAGAGGATGGACTATTCTATTGGTAGGCATCCTGAGTTCCGTTACAAAACAGAGTTTCAGAGTCATGAGCCAGAG

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 2
--gtgagttcctttttcttctgcaaga---tttgtttcgaaaaaatgtt-------atgtgctgtaacgcactc----ttgcaaaatgtt-----------actttcagCATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGT---TAGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAG
    || |   |||| ||| ||||||    ||||| || ||||||           ||    ||| | |||||     ||| || ||||            || | |||||||| || || || | |||| | |||  |  ||| ||  |  |   ||||||||||||||| || || |||||||| ||||||||||| |||||||||
gtaagactgatttttgcttatgcaagtgtttttgtgtcaaaaaaacaaacaaacagattccttgttatgcacttaattttgtaacatgtatgtttgctgaaacatgcagCATGGTGGATCAAGTAGGGATTTGGAGAGGGTGGACTATTCTATTGGTAGGCATCCTGAGTTCCGTTACAAAACAGAGTTTCAGAGTCACGAACCAGAG

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 2
---------------------gtgagttcctttttcttc-----tgcaagatttgtttcgaaaaa----atgttatgtgctgtaac-----gcactcttgcaaaatgttactttcagCATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTT---AGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAG
                     |  | ||| ||| |         | | |  || | ||  ||| |    |  |||    ||  |         |    || | | ||| |||| ||||||   || || || | |||  | |||  || ||| ||  |  ||   || ||||||||||| || ||||||||||| |||||||||||||| || |||
gtaagtctaattttttcttcagcaatttcttttataactaaaattactaacttaggttttaaagattctactttacacccttaattttctaatatctatgtatactgtaacttgcagCATCACGGATCAAGAAGGGACTTGGAGAGGATGGACTATTCTATTAGTAGACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAG

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G20830.1 (Glycine max), 3'ss of exon 2
---------------------gtgagttcctttttcttc-----tgcaagattt--gtttcgaaaaaat--gttatgtgctgtaacgcactct--------tgcaaaatgttactttcagCATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAG---GCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAG
                     |  | ||| ||| |         | | | | ||  | || |||| | |   || |   |  | |    ||||        || | | ||| |||| |||||| | || || || | |||  | |||  || ||| ||  |  ||||    ||||||||||| || ||||||||||| |||||||||||||| || |||
gtaattctgattttttcttcagcaatttcttttataactaaaattactaaacttaaggtttgaaagattccattttacacccttaatttctctaatatctatgtatactgtaacttgcagCATTGCGGATCAAGAAGGGACTTGGAGAGGATGGACTATTCTATTAGTAGACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAG

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|116411283|gb|EG453875.1|EG453875
EST:     GTGACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAAAGAT                         CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAGGCAT
genomic: GTGACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAAAGATgtgagttcct ... ttactttcagCATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAGGCAT
EST: gi|125312732|gb|EL326817.1|EL326817
EST:     ACCGT-GGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAAAGAT                         CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGNTTACCCAGTTAGGCAT
genomic: ACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAAAGATgtgagttcct ... ttactttcagCATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAGGCAT
EST: gi|116432328|gb|EG474920.1|EG474920
EST:     GTGACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAAAGAT                         CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAGGCAT
genomic: GTGACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAAAGATgtgagttcct ... ttactttcagCATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAGGCAT
EST: gi|116478422|gb|EG521014.1|EG521014
EST:     GTGACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAAAGAT                         CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAGGCAT
genomic: GTGACCGTGGGGGCCGAGTAGTTCTTTTTGAAAGGACAGATACTAAAGATgtgagttcct ... ttactttcagCATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAGGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttcgaaaaaatgttatgtgctgtaacgcactcttgcaaaatgttactttcagCATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAG
                      ctgtaac  putative branch site (score: 3)
                                             ttactttc  putative PPT
       aaaaaatgttatgt  TA-rich tract