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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactgattcatacactgttagtctctcgtgtttctgacggtctatattttatacttaagtcggaatcattgatcgaggttagctcataaactctctgtgcattgatttcctgaaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG

Basic information

species Arabidopsis thaliana
transcript AT2G17390.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G17390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: AC215244.3_FGT002 (Zea mays), 3'ss of exon 5
gtaaactgattcatacactgttagtctctcgtgtttctgacggtctatattttatacttaagtcgg-aatcattgatcgaggttagctcataaactctctgtgcattgatttcctgaaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG
              |||   ||  ||| ||    |||  |     || | ||   || |             |||||   | |  ||| |     |||       |  | ||| ||   |||  ||||| | ||    ||  | |    ||| |   |||| ||||||||||||||||| ||||| |  || || |||||||||||||| ||||| |||
-------------aacatcatttatctgtc----ttcacagtaaatacagttgccaccttgcctactgggttttgattttgatatgctgacgttgtcttc-----taaaattcatg---caat-agGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG

upper sequence: AT2G17390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G47830.1 (Glycine max), 3'ss of exon 6
gtaaactgattcatacactgttagtctctcgtgtttctgacggtctatattttatacttaagtcggaatcattgatcgaggttagctcataaactctctgtgcattgatttcctgaaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG
                   | ||  |  || |  || ||    | | || |  |  | |       | |   | |||  |  |   |  | || | | || |   | |  |  |  || |   |||| ||||||  |||  | || |||||||   |||| ||||||||||| || || ||||| ||||||||||||||||| |||||||| ||||||
-------------------gctaagccatc-tagttatggtattgtttaatccagcccttgtctttagtg--tcatcaggtatgatt--tgaaatatttgagagctaaaattttacac-atttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG

upper sequence: AT2G17390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G12950.1 (Glycine max), 3'ss of exon 6
gtaaactgattcatacactgttagtctctcgtgtttctgacggtctatattttatacttaagtcggaatcattgatcgaggttagctcataaactctctgtgcattgatttcctgaaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG
                  || ||  || ||  |||   |      || |||      ||   |  |  ||||||     | ||      | || | | || |   | |  |  || || |   |||| ||||||  |||  | ||  ||||||   |||| ||||||||||| || || ||||| ||||||||||||||||| |||||||| || |||
------------------tgctaagctgtctagttatggtattgttaaattcagccattctcttagtgtcattgggtatgatt------tgaaatatttgagagctaaaattttgcac-atgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGTGAG

upper sequence: AT2G17390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv03s0038g04270.t01 (Vitis vinifera), 3'ss of exon 6
gtaaactgattcatacactgttagtctctcgtgtttctgacggtctatattttatacttaagtcggaatcattgatcgaggttagctcataaactctctgtgcattgatttcctgaaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG
                    ||| ||| |      |   |  ||  |||| || |   |   |     || ||  | |   |||||     ||   |    |  |  | |   |     ||  ||||||||||   |||  | || |||||||   |||||||||||||||| || || |||||||||||  ||||||| |||||||| || || |||
--------------------ttattctattaataatgacaaagtgaatatattttgtatctttttagttcgtttttagcaattagc-----aaggttgaaagtttccactctatttgtaaattagGGTTTGAAGAATGCACTTGCCTCTGGTGCCGACAAAGATGAAGAAGATTCAGAGGGAAGGACTGCACTGCATTTCGCATGTGGGTATGGTGAG

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|164166139|gb|ES158680.1|ES158680
EST:     AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGAC
genomic: AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAGgtaaactgat ... aaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGAC
EST: gi|86081509|gb|DR377266.1|DR377266
EST:     AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCT
genomic: AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAGgtaaactgat ... aaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCT
EST: gi|164196814|gb|ES051584.1|ES051584
EST:     AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAG
genomic: AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAGgtaaactgat ... aaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAG
EST: gi|124794969|gb|EH884648.1|EH884648
EST:     AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAG                         GGTTTGAAAGCTG
genomic: AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAGgtaaactgat ... aaccaaccagGGTTTGAAAGCTG
EST: gi|124815907|gb|EH900773.1|EH900773
EST:     ACCAGACCGCTAGTCTTGGTGATGTCGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCT
genomic: ACCAGACCGCTAGTCTTGGTGATGTCGAGgtaaactgat ... aaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCT
EST: gi|301502460|gb|HO208000.1|HO208000
EST:     AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCT
genomic: AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAGgtaaactgat ... aaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCT
EST: gi|125285016|gb|EL299101.1|EL299101
EST:     AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGGAA
genomic: AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAGgtaaactgat ... aaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAA
EST: gi|125274385|gb|EL288470.1|EL288470
EST:     TCTTGGTGATGTCGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCT
genomic: TCTTGGTGATGTCGAGgtaaactgat ... aaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCT
EST: gi|124855012|gb|EH939449.1|EH939449
EST:     AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAG                         GGTTTGAAAGCTGCCTTGGCATCTGGTGGG
genomic: AAGAGGAAGAGTCTATTGTTCACCAGACCGCTAGTCTTGGTGATGTCGAGgtaaactgat ... aaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatcgaggttagctcataaactctctgtgcattgatttcctgaaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG
                                cattgat  putative branch site (score: 4)
                                 attgattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactgattcatacactgttagtctctcgtgtttctgacggtctatattttatacttaagtcggaatcattgatcgaggttagctcataaactctctgtgcattgatttcctgaaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA