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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatagatacttgcacatctcttttaggaactaagaacttgtttatgactagttgaataaataagaacttaatccgtttgtttcggaatcttaccagTGGATGTAGGGCAGATGCAAATGAGGCAGTTATGGTTCTCCTCCCATCTAACATAACTGTTTTCACCCTTGACTTCTCGGGGTCAGGCTTATCTGAGGGT

Basic information

species Arabidopsis thaliana
transcript AT4G17150.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 4
----------------------gtacatagatacttgcacatctcttttaggaactaagaacttgtttatgactagttgaataaataagaacttaatccgtttgtttcggaatcttac--cagTGGATGTAGGGCAGATGCAAATGAGGCAGTTATGGTTCTCCTCCCATCTAACATAACTGTTTTCACCCTTGACTTCTCGGGGTCAGGCTTATCTGAGGGT
                       |   | ||| |||  | |    | |       | |  | |  ||| |  ||| |  | |           | ||  || ||  |  | |   |    ||||||||||||||||||||| ||||| || | | |  |||| || || || || || |||||||| |||||||||||||||||||||||||||||||| || 
gtatttgttattaaaatggttattgtcttgatgcttttaaaaaattgtatatgtgtgatcattattttttagctattctattcttctcccttgtgatatgtgtgcatacgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA

upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 4
gtacatagatacttgcacatctcttttaggaac-----taagaacttgtttatgactagttgaataa----ataagaacttaatccgtttgtttcggaatct-----------tac-------cagTGGATGTAGGGCAGATGCAAATGAGGCAGTTATGGTTCTCCTCCCATCTAACATAACTGTTTTCACCCTTGACTTCTCGGGGTCAGGCTTATCTGAGGGT
|||| | | || |   |   ||||| |    |      ||| || |||| ||||  |  |   | |      ||   | |  || | | |   | |  || |           |||       ||||||||||||||||||||| ||||| || | | |  |||| || || || || || |||||||| |||||||||||||||||||||||||||||||| || 
gtactt-gttattaaaatgactcttgtcttgatgcttttaaaaaattgtatatgcatgatcatagagttttttagctattctattcttctcccttgtgatatgtgtgcatacatacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA

upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 2
--------------------------------------------gtaca---tagatacttgcacatctcttttaggaactaagaacttgttt---atgac-tagttgaataaataagaacttaatccgtttgtttcggaatctta------ccagTGGATGTAGGGCAGATGCAAATGAGGCAGTTATGGTTCTCCTCCCATCTAACATAACTGTTTTCACCCTTGACTTCTCGGGGTCAGGCTTATCTGAGGGT
                                             |||    || |  | |  | | |  ||||    | |      || ||    |||||  | |      | |     |||  ||| | ||| |  | || |         ||||||||||||||||||||| ||||| || ||| |  |||| || ||||| || || |||||||| || ||||||||||| ||||||||||| ||||| || 
gtatgccaatttttatggatactgctatcactgcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttttttttcagaatgacacactcattccattcttctctttttccatatgtatgtgcatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGTTGTTATTCTTCTTCCATCAAATATTACTGTTTTTACTCTTGACTTCTCAGGGTCAGGCTTGTCTGATGGA

upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 4
--------------------------------------------gtaca---tagatacttgcacatctcttttaggaactaagaacttgttt-----atgactagttgaataaataagaa---cttaatccgtttgtttcggaatctta--ccagTGGATGTAGGGCAGATGCAAATGAGGCAGTTATGGTTCTCCTCCCATCTAACATAACTGTTTTCACCCTTGACTTCTCGGGGTCAGGCTTATCTGAGGGT
                                             |||    || |  | |  | | |  ||||    | |     ||| |||     |||||    | | |  ||         || ||  || |||    | |   |    ||||||||||||||||||||| ||||| || | | |  |||| || ||||| || || ||||| || || |||||||| |||||||||||||| ||||| || 
gtaagcaaatttttatggatactgctatcactgcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttctttttttcagaatgacacactcattccattcttctcttttcatatgtatgtacatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTTATTCTTCTTCCATCAAATATTACTGTCTTTACTCTTGACTTTTCGGGGTCAGGCTTGTCTGATGGA

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|19878908|gb|AU239739.1|AU239739
EST:     TCTCGGGAGGATACTCCTCTCCCCTGTGTTATATACTGTCATGGCAATAG                         TGGATGTAGGGCAGATGCAAATGAGGCAGTTATGGTTCTCCTCCCATCTAA
genomic: TCTCGGGAGGATACTCCTCTCCCCTGTGTTATATACTGTCATGGCAATAGgtacatagat ... atcttaccagTGGATGTAGGGCAGATGCAAATGAGGCAGTTATGGTTCTCCTCCCATCTAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgactagttgaataaataagaacttaatccgtttgtttcggaatcttaccagTGGATGTAGGGCAGATGCAAATGAGGCAGTTATGGTTCTCCTCCCATCTAACATAACTGTTTTCACCCTTGACTTCTCGGGGTCAGGCTTATCTGAGGGT
                        acttaat  putative branch site (score: 4)
                                              tcttacc  putative PPT
          ttgaataaataagaac  TA-rich tract