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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT

Basic information

species Arabidopsis thaliana
transcript AT1G17720.2
intron # 8
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 8
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatc-----acagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
                |  |  || |||  |  ||    || | ||   || | ||| | |  | |  |||  |     |||||  |  |||   |   ||     ||   |    | | || |    | |  | | || ||   || | | ||  |  |    |    | |       | |     |||||||||| ||||  ||||||||||| |||||||| || || ||||||||||| || ||||| || ||||| ||||| |||| |||||| |||||||| |||
--------------gttagtaattcatctta--tgccttttacctgcaacattttatccgtgtgtactggaggtagt--cgtggacttctttt-gacggttgggacttggggctgcataagattctctattctatactagtaa--tagaatgtcacaatatcagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 8
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
             | |  | ||    | | |  |  || | | |  |||  ||  ||  || ||||||  || |       | | |  | ||  ||  || |   | | |      |  | | ||  | ||| | |  |||  ||  ||| |  |  | |      | ||  || |  | |  ||||||||| || |  || |||||||| || ||||| ||||| |||||||||||||| ||  |||||||||| |||||  ||| |||||| ||  |||| |||
------------gttagtaaccccc-ttgcacttcctaatggaacattt--at-cattgtttagaaggaaatgt-------tcgatggaattaaaaagttgcaaatgttt----gaagttaatttttatatggataa-aatttgcacaagctgttctctaaaataaagtgc-gcattctgt-gcagATTTGAGGAGCATGAGGCACCTGGATCGAGATCCTTTTTTACAGAGATAATTGCATCGGTTTCAGATATAAAATTTGCAAGGGATGGAAGGCACATTCTT

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 8
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaa--atgacttggaaatgaagattaataggc---taaagtttctgaccactgaccattgttgcttcatat-cacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
                                                               ||        |   |||      || ||| |||| ||   | |   || |  | |  |  |  |||       |  |     |    ||   ||| | |  | |  | |||  |  |  || |    || |||||  | |  || || || |||||||||||||| || || ||||| || ||||| |||||||| || || || || |||||||||||| | || || 
-------------------------------------------------------------gtgagttttcatttgttactcatactctttttcaatattcaacatagtttatttggatgagcatctggtggattggcctgtcttgttcgtactattttttatta-tagctattcctattctatgtgtgtagCTTTGAGCAGCATGAGGCCCCAGGTTCAAGATCATTCTTTACTGAGATTATAGCCTCGATTTCAGACATAAAGTTTTCCAAGGATGGGAGACATATTCTC

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
                                  | ||||  |     |  |  |  | | || |      | ||| ||   ||      ||  | ||| ||  || |  || |   ||  | ||  |  | |   || || ||  |  || |        | |  | ||  || || | |  ||||||||| || |  ||||||||||| |||||||| ||||| ||||||||||| || ||| |||||||||| |||||  ||| |||||| ||| |||| |||
----------------------------------gttagtaaccccccttgaacttcagt-aacattattgt-tgattagaaggcaatgcttagattttatcatttctaatggctacaaacattttaagttta---tttattggtcatggtcttatctggttta--actggggcatcttgtt-cagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 8
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaa-tacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
                                                | |   | || || | |     ||||    ||| |||    | |  ||| |     ||   ||| |||   ||  | |  || |     |   |   |||   |||||      |  |  ||||  |||| | |   || |||||  | |  || || || |||||||||||||||||||| ||||| || || |||||||| || || ||||| || |||||||||||  | || || 
-----------------------------------------------gtgagcttttatttcacactaacatatactctacttggag--aatatcaagtgaatactgcccttctcaattat--cctataagtt----tcgttgtacta---tttcta-----tacctgttgt--cttcttgt---agCTTTGAGCAGCATGAGGCCCCAGGTTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTC

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaa-atgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
                                                                         |  | |  |  |    |  || || | |  | | |  |      ||| | ||  |      |  ||| ||   ||   ||| |||    | || |  |   | | | |  |||||||||| ||||  ||||||||||| |||||||| || || ||||| || ||||| |||||||| ||||| || || |||| | |||| | ||| || |||
-----------------------------------------------------------------------cctagacaactaaggctgtagcctatgtataacatatgct------aataatttatattgcagaagttatta---tatgttttatga--gttaacaaagg---cctaaaa--acagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 8
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
|| || | |    | | ||   |||||     |   ||      |||| || ||||  || |    | | ||||       |||||  ||    |  || ||  || || |   | |  |  |||| |                       || | |   |||  |||   | |||        || |||||  | |  || || || || ||||||||||||||||| ||||| || ||||||||||| || || || || || |||||||||||  |  | || 
gtgagcttttagttta-cactttttatttcctacaata------tgtt-cagtatactct-acttggagaatat-------tgggtggatactgaccttatcaattatccta--aaagtttccttgta-----------------------tttttatacctgttcatgtcttctt------gtagCTTTGAGCAGCATGAGGCCCCAGGCTCAAGATCATTTTTCACTGAGATTATAGCCTCAATTTCGGACATAAAGTTTTCGAAGGATGGGAGGCATCTTCTC

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
                                                                       | || ||||   |           ||||||||   | ||  |    | | | |     |||    ||  |  ||   ||  ||     || ||  ||| ||   |      |||||||||| ||||  ||||| ||||| ||| ||||||||||||||||||| ||||||||||| ||||| || |||||    |||||||| ||||| ||||||
----------------------------------------------------------------------ttttgcatacaaagaaaagc-----atttttctggatcctatt--atatttattcatttatgtgatttcttttgcggtagactc-----acagaaaattattttctg----tacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 8
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttct-tgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
                                                                                      | |     |||||||||     || |   |   |||| ||           |||||||     ||  ||| |  |   |  |   |||     |    ||||||||| |||| |||||| || || || |||||||||||||||||||| ||||| || || ||||| || |||||    |||||||| ||||||||||| 
--------------------------------------------------------------------------------------tgaagcagaatttttctgaagcctgttatatgcatgaatttatgtatttttttaatagctggtagactctaataaacaat-acccttggcatttgatgcagATTTGAGGAACAGGAAGCCCCAGGGTCCAGATCATTTTTCACAGAGATTATTGCTTCTATCTCAGACATAAAATTTGGGAAGGATGGAAGATACATACTA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 8
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
                                                                       |    | | |      |||||    | |    | | |  | |  | | | | ||  |  |||    |  |  | |||| |  | ||  | |  |  ||||           |||||||||| ||||  ||||| ||||| || |||||||||||||||||||| || || ||||| ||||| || |||||    |||||||| ||||| ||||||
----------------------------------------------------------------------ttgcatacaaggaaaaccatttt---tctggagcctattatatatgtattcattt--atgtgatttgttttgcggtaaactcacagaatattaccttttgt-----------acagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 8
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctct--tttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
                                                                                        |     |||||||||      | || |  | |   | ||    ||     ||||||      ||  ||| |  |   |  |   |||     |    ||||||||| |||| |||||| || || || |||||||||||||| ||||| ||||| || || || || || |||||    |||||||| ||||||||||||
---------------------------------------------------------------------------------------gaagcagaatttttctgaagcctgttatatgtatgaatttatgtattttttttaatacctggtagactctaataaacaat-acccttggcatttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTATTGCTTCTATCTCGGACATAAAATTTGGGAAGGATGGTAGATACATACTT

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgacc--actgaccattgttgcttcatat-cacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
                                                                                     | ||||    ||                 | ||     ||| |  | ||  ||  ||   ||  | |  |  |   |     || || |  | | |     ||| ||||| ||||  || |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || |||||||| ||||  ||||| 
-------------------------------------------------------------------------------------tgcatt---gatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttat-ttagtgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC

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|116478423|gb|EG521015.1|EG521015
EST:     CGTTTGATTGATATGCGTCAATCAGCTCTGTGTGATTCTCATACGAAATT                         ATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAAT
genomic: CGTTTGATTGATATGCGTCAATCAGCTCTGTGTGATTCTCATACGAAATTgtaagttctg ... catatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAAT
EST: gi|301502468|gb|HO208008.1|HO208008
EST:     CGTTTGATTGATATGCGTCAATCAGCTCTGTGTGATTCTCATACGAAATT                         ATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAAT
genomic: CGTTTGATTGATATGCGTCAATCAGCTCTGTGTGATTCTCATACGAAATTgtaagttctg ... catatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
                           cactgac  putative branch site (score: 2)
                                       ttgcttc  putative PPT
              taaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT