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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatcaatctccatcttgcttatatctagcagctgaatcttctgtttctactttagaagcagctgttattgtgttagagcatctgatgagtattgcttgatactttataagtgagagctaataaggatttcgtttgttatgctttgaagttgtgtttagtaattagtttcgattatgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT

Basic information

species Arabidopsis thaliana
transcript AT4G01370.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 3
gtatgcatcaatctccatcttgcttatatctagcagctgaatcttctgtttctactttagaagcagctgttattgtgttagagcatctgatgagtattgcttgatactttataagtgagagctaataaggatttcgtttgttatgctttgaagttgtgtttagtaattagtttcgattatgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT
                                                                                      |  |  | |||   ||| |||      ||| | |  || |            || |||  | |  | |     ||  ||  |  |  |  || |   |||||||  ||  ||||||||||||| || ||||| |||||||| || ||||| ||| ||||||| || ||| |||| || ||||||||| |||| ||||||||||
-------------------------------------------------------------------------------------acaaagaactatattttggtacggagggagtaata--tattgcttcacaacaatgatatattctataatctatatttcta--tgttccccctttttccttgcagTACTTCTTGTATCAGTTGTTACGAGGGCTAAAATATGTGCACTCAGCAAATATATTGCACCGCGATCTGAAGCCGAGCAATTTGTTCCTAAATGCAAATT

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 3
gtatgcatcaatctccatcttgcttatatctagcagctgaatcttctgtttctactttagaagcagctgttattgtgttagagcatctgatgagtattgcttgatactttataagtgagagctaataaggatttcgtttgttatgctttgaagttgtgtttagtaattagtttcgattatgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT
                                                                             |    | || | |||  |  |     |  ||| |        |||  ||||   | |  | | || |   ||| ||       ||  || |  |||      | |    |||| |||||||||||| ||||| || |||||||||||||| |||||||| ||||| ||||| |||||| | || ||||| ||||||||  ||||||| ||||
-----------------------------------------------------------------------------tgcatggatttcatg--tggtctccaaggcttcaggcactgtagc--ataat--tcttatattttctttcttgcagccactcataagaactttttt------tttgccccagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGAGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G07270.1 (Glycine max), 3'ss of exon 3
gtatgcatcaatctccatcttgcttatatctagcagctgaatcttctgtttctactttagaagcagctgttattgtgttagagcatctgatgagtattgcttgatactttataagtgagagctaataaggatttcgtttgttatgctttgaagttgtgtttagtaattagtttcgattatgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT
                                                                                  | |  | |||  |  |  || |  ||| |        |||  ||||   | |  | | || |   ||  ||       ||  || |  |||   || ||     |||| |||||||||||| ||||| || |||||||||||||| |||||||| ||||| ||||| || ||| | || ||||| ||||||||  ||||||| ||||
-------------------------------------------------------------------------------catggacttcatg--tggtctttaaggcttcaggcactgtagc--ataat--tcttatattttctttcttacagacactcataagaacttttttt--ttttgccc--cagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGTGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 3
gtatgcatcaatctccatcttgcttatatctagcagctgaatcttctgtttctactttagaagcagctgttattgtgttagagcatctgatgagtattgcttgatactttataagtgagagctaataaggatttcgtttgttatgctttgaagttgtgtttagtaattagtttcgattatgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT
                                                                     || |||| ||  |  |       |  | | ||    | |  ||  ||       |  || |||    ||| |  ||  ||  |||   |  |  |||           ||  |||| |||| |||||||||||||||||| || || ||||||||||| || ||||| |||||  |||| || ||| | || |||||||| ||||| |||||||| || |
-------------------------------------------------------------------cctttttgttttgaatta------aaacagtactcagca-tacattggtctatataaccaaagat---atttatactgtcttacagt---gactgataa---------gatacattttccagTATTTTCTGTATCAGTTGTTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACT

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 3
gtatgcatcaatctccatcttgcttatatctagcagctgaatcttctgtttctactttagaagcagctgttattgtgttagagcatctgatgagtattgcttgatactttataagtgagagctaataaggatttcgtttgttatgctttgaagttgtgtttagtaattagtttcgattatgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT-
                                                                     || |||| ||  |  |    | ||||| | | | |||| ||    ||       |  || ||| |      |||| || |      |||  |  |||           ||  |||| |||| |||||| ||||||||| | || || ||||||||||| || ||||| |||||  |||| || ||| | || |||||||| ||||| |||||||| || | 
--------------------------------------------------------------------ctttttgttttgaatta---aaagagtact-catcatacattg---gtttatataaccaaagatat------ttatactgtctcacagtgactgataa---------gatacattttccagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACTG

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
gtatgcatcaatctccatcttgcttatatctagcagctgaatcttctgtttctactttagaagcagctgttattgtgttagagcatctgatgagtattgcttgatactttataagtgagagc-taataaggatttcgtttgttatgctttgaagttgtgtttagtaattagt-----ttcgattatgtttt--gcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT
                                                                                               | ||   |||  ||| ||||||  |   ||| |    ||  || || | | || |||    |   | ||   | | |     | | ||| |  | |  |||||  || ||||||||| |||| || || || |||||||| || ||||| ||||| |||||||| |||||||| || || |||||||| |||||||||||||
-----------------------------------------------------------------------------------------------actgtgggat-ttttgtaagtgcaaatataacatcttttctgtatgattt-ctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT

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|86026213|gb|DR321966.1|DR321966
EST:     TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGG                         GTTTTTCTGTATCAGGTGTTGCG
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTTCTGTATCAGTTGTTGCG
EST: gi|86026217|gb|DR321970.1|DR321970
EST:     TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGG                         TTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAAT
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAAT
EST: gi|86026226|gb|DR321979.1|DR321979
EST:     TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGG                         TTTTT-CTGTAT
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTTCTGTAT
EST: gi|116416232|gb|EG458824.1|EG458824
EST:     TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGG                         TTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAAT
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAAT
EST: gi|86026211|gb|DR321964.1|DR321964
EST:     TCCACCARATTATTCGCTCTAACCA-CCCTTAACTGATGATCATTGTCGG                         TTTTTTCTGTATCAGTTG
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTTCTGTATCAGTTG
EST: gi|86026216|gb|DR321969.1|DR321969
EST:     TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGG                         NNNNNNNCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAA
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTT-CTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAA
EST: gi|86026224|gb|DR321977.1|DR321977
EST:     TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGG                         TTTTTTCTGTATCAGTT
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTTCTGTATCAGTT
EST: gi|86026227|gb|DR321980.1|DR321980
EST:     TCCACCAA-TTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGG                         TTTTTTCTGTATCAGTTGTTGCGT
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTTCTGTATCAGTTGTTGCGT
EST: gi|86026230|gb|DR321983.1|DR321983
EST:     TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGG                         TTTTTTCTGTATCAGTTGTT
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTTCTGTATCAGTTGTT
EST: gi|86026212|gb|DR321965.1|DR321965
EST:     TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGG                         TTTTTTCTGTATCAGTTGTTGCGT
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTTCTGTATCAGTTGTTGCGT
EST: gi|86026206|gb|DR321959.1|DR321959
EST:     TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGG                         TTTTT-CTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCA
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCA
EST: gi|116451512|gb|EG494104.1|EG494104
EST:     TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGG                         TTTTTTCTGTATCAGTTGTTGCGTGGG
genomic: TCCACCAAATTATTCGCTCTAACCAACCCTTAACTGATGATCATTGTCGGgtatgcatca ... tgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtttgttatgctttgaagttgtgtttagtaattagtttcgattatgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT
                        tttagtaattagttt  TA-rich tract