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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

Basic information

species Arabidopsis thaliana
transcript AT1G17720.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
---------------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagct--aaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
                            |     |||||||  |   |||     ||    |  |||  ||  | ||     |  || ||  || ||        |||||||||| ||| ||||||||||||| ||||| |||||||| |||||||| ||||  || || ||||||||| | |||||||| |||||||||||
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
gtgagagcttctt--tctgtggcatcttttatttgttgattctg-----tgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
|||| || ||| |   |||    ||     |  |||  ||  |      |||   || ||||   |||  |  |||   |  |||||||| || ||||||||||||||||| || || ||||| |||||||| |||||||||||||| |||||| |  | || ||||| || ||||||||
gtga-agtttcgtaacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
gtgagagcttctttctgtggcatcttttatttgttgattctgtg-ttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
||||||  || |           ||   |       ||    ||  ||| |  ||| |  | | |  | ||     || ||| |||| ||||| ||||| || ||||| || ||||| ||||||||||||||||| ||||| |||||| |    || ||||| ||||| ||  |
gtgagactttgtcaaccgaatgactaaaaagaagccatatgatgactgatacataatctagctgtactctaat---tttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 10
----------------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccgg--ttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
                             |    | |||||| ||    ||   | |    |  ||| | || || |  | |||      |||| ||||  ||   ||||| |||| ||| |||||||||||||||| || ||||| ||||||||||||||||  ||||| |||||||| || |||||||| ||||| |||||
gtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacat--atttt-tgctggagccaaactgatccatgtgttacttggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
------------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccgg--ttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
                         | |  | |  ||  |   |||   |  ||        | | || || ||   | |      |||| |||| |     ||||| |||| ||| |||||||||||||||| || || || ||||||||||||||||  ||||| |||||||| || |||||||| ||||| |||||
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
-------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
                    | || | |   || ||       || || |  ||  |   ||  | |  | | |  |  |||||||| | |  |   ||||| |||||| |||||||||||||||| ||||||||||| || || |||||||| ||||| ||||||||| |  ||||||| |||||||||||
gttagattcctgtgtttagataagtgatgaattatgaatttcattctactgctttgtcgagttataactggttat-attttatgtttgaacatgc--cagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 10
-----gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
      | || | |   || ||     |||||    ||||   |||| |||  || ||    | | | | | ||     ||  ||||| || ||| ||||||||||||| || ||||| ||||| || || |||||||| ||||| ||||||||| | |||||||| |||||||||||
gtttgataagtgatgaattatg-aatttctttctactgttttgtctgagttataa-ctggttatgctttttgtttgaacgtgccagCTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
-------gtgagagcttctttctgtggc-atcttttatttgttgattctgtgttgaaagctaaccac--gttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
             | || | |  ||    | |  | | ||  || | || | |  |    ||   ||  | |   ||||    ||   ||||| || ||| ||||||||||||| || || |||||||| |||||||||||||| ||||| ||||||||| | ||  |||| |||||||||||
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggc--cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
gtgagagcttc-tttctgtggcatcttttatttgttgattctgtgttgaaagctaaccac--gttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
|| |||    | | | ||    | |  | | ||  || | || | |  |    ||   ||  | | | ||||    ||   ||||| || ||| ||||||||||||| || || |||||||| |||||||||||||| ||||| ||||||||| | ||  |||| || ||||||||
gttagattcccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaactggctcttttttttttggc--cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
--------------gtgagagcttctttctgtggcatcttttatttgttgat-tctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
               | |||      ||     | |    || |   ||  | ||||  |   ||  | |||   |  |  ||| |     | ||| | || ||| ||||||||||||| || ||||||||||||||||| |||||||||||||| |||||| || | ||||| ||||||||||||||
gtgagcttgctttcctcagaaaagtcttacacagaacaacttctacattactctctgcatgctaattttaccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------gtgagagcttctttctgtggc--atcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
                   |    ||||  | |  ||     ||  |||   |    || | | |    | ||    |     | ||     |  |||||||| || ||||| ||||| || ||||||||||| || || ||||| |||||||| ||||| |||||  || | || ||||| ||||| |||||
gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgt-agaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
-----gtgagagct-tctttctgtggcatcttttatttgtt------gattct---gtgttgaaagctaaccacgtta---tgttttac-ccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
      |  | | | | ||| | ||| ||  ||   ||| |      ||| |    ||| ||  |    || |   ||   ||||||    || |||||||| | |||| |||| ||||||||||| || || || || |||||||||||||| |||||||||||  || | ||||| || ||||| |||||
atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
----------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
                      |  ||| |       | | |    || | |||||    | ||| |||||  || ||     |   ||        |||||||| || ||||| ||||| || || || ||||| ||||| |||||||||||| | |||||||||||  || | |||||||| ||||| |||||
cttcaatcaaaatataactgaaggcagaacaggggaat-tagttggttatgtttgtgtcgtttgtattgaa--ctcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG

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:     ATTCTGGTCCGGTCGCATCTTACCAGGTTCATGAACATCTGAGACCCAGG                         CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGT
genomic: ATTCTGGTCCGGTCGCATCTTACCAGGTTCATGAACATCTGAGACCCAGGgtgagagctt ... ccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGT
EST: gi|301502468|gb|HO208008.1|HO208008
EST:     ATTCTGGTCCGGTCGCATCTTACCAGGTTCATGAACATCTGAGACCCAGG                         CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGT
genomic: ATTCTGGTCCGGTCGCATCTTACCAGGTTCATGAACATCTGAGACCCAGGgtgagagctt ... ccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
                       agctaac  putative branch site (score: 2)
                                       ttttaccc  putative PPT
                                  ttatgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA