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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG

Basic information

species Arabidopsis thaliana
transcript AT3G23990.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
gttagtccatgttataatgttt----tgggagtc---ttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagcta--attgtgttt-----agATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
       ||    || |||||     ||| |||    ||  | |  ||| ||    |   | |  ||  | || | || | |  |   |  ||    |||     |||| |||||||| |||||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||| || || |||||||||||| ||||||
------acacacaatgatgttgagaatggaagttgaattgcactgctaggagtggtgccctgaa-gttatattttgacctgtatatgcatcatgacctttcctacagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 13
---gttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaa----ttgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
   |   |  |||  ||| |   ||   || |||    |   |       ||   | | | || || || |   ||    |  |      ||   |||||||||| ||||| |||||||| || |||||||||||||| || |||||||| |||||  | ||||| || ||||| || || || ||||||||| ||||||
agtggcggaacattctattactattactgattctagtgactgtcctgagttgtgagcatgggtattatttttttttaaaaaaattggatctttcctttagATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
----------------------gttagtccatgttata----atgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaat---tgtgttt--------agATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
                      |||     |||  | |    ||||||      | ||       | | |     |||    ||||||       | ||   ||  |  |   ||||  |        ||||||| ||||| || ||||| ||||||||||||||||| || ||||||||||||||  ||||||| |||||||| || ||||||||||||||| ||||||
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 12
-----------------------------------gttag--tccatgttataatgttttgggagtcttagaatcatagcagcctgg------ttgtaagtgtcttgttata-acttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
                                   | |||  | |||||| |  | || |       ||  ||| |  |   ||||        ||  | |  ||  || |   | | ||     |    |   |||||||||||||| || ||||| ||||||||||||||||| || ||||||||||||||  ||||||| |||||||| || ||||||||||| ||| ||||||
gtgaggttattgacctactgtatgtatttacgaatggtagattacatgttcttgttttatatcgtaattgtaataactgttacctgtggctctctgatatttcctgattttgtgcctatgtgtgcatcctttcctagATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
-------gttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgta-agtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
       | ||   |   |  | |    |  |    ||    | |||  | |   |||| |  | || |    | |||| | || | ||     | |  ||||||||||||| |||||||||||||||||||||||||| || |||||||||||||| || ||||| ||||| || || || || || || ||| || |||
gggggccgctacggccgctattgacaactatgatccctggtgaacatccctgtggggttctgcaatggcaaaat-taacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
----gttagtccatgttataatgttttgggagt-----cttagaatcatagcagcctggttgta-agtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
    |        ||| ||  || ||   |  |     ||    | |||  ||    |||| |  | ||      | | || | |  | ||     | |  ||||||||||||| |||||||||||||||||||||||||| || |||||||| ||||| || ||||| ||||| || || || || ||||| ||  | || |
gtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgcaatggaaaaat-tgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 13
gttagtccatgttataatgttttgggagtcttagaatcatagca---gcctggttgtaag----tgtcttgtta----taacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
||| ||  || | |   |   |||   |   |  | || || |    || |  |  || |    |||| || ||    |||| |||| | |      | |  ||||||||||||| ||||| |||||||||||||||||||| || |||||||||||||| || ||||| || || ||||| || || ||||| ||  ||||||
gtttgtttatttgagtttaccttgcttgctgttaagtcttatctggtgcttcatcatatggttttgtcatgataaaattaacatctgaaaccttacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
gttagtccatgttataatgttttgggag-tcttagaatcatagcag---cctggttgtaag----tgtcttgttataact----tctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
||| ||  || | |   |   |||   | | |||| ||  || | |   | |  |  || |    |||| || || ||||    |||| | |      | |  ||||||||||||| ||||| |||||||||||||||||||| || |||||||||||||| || ||||| || || ||||| || || ||||| ||  |||| |
gtttgtttatttgagtttaccttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------------------------------gttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgttt--agATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
                                                     | |   || |   || |||  ||| |  || ||| |||| |         | ||  | | |    | |   |    |  |  ||   |||  |||| |||||||| ||||||||||||||| ||||||||||||| || || ||||||||| | ||||| ||||| ||||| || ||||| || ||| ||||||
gtctgtatcaatttacaaatccccaacattactgtctaggcttgttgaggctctaaactcaggagctactgtactggta--ctcagattcatggggaatgttatctagatatatataaaaatggtggaaaattgcttccctttgcagATAGGAGGAGCTAGTGAAGCTGAAGTTAGTGAGAAGAAAGATAGGGTTACAGATGCTCTAAATGCTACTAAGGCAGCTGTAGAAGAAGGAATTGTACCAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------gttagtccatg--ttataatgttttggga----gtcttagaatcatagcagcctggttgt----aagtgtcttgttataacttc-tggagctaattgtg---------tttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
                             |||    | |  ||| | | |||| |||    ||| |  |     |   |  | ||| |    || |||     || |      ||  ||||||  |          | ||||| |||||| | |||||||  |||||   |||||| |||||  | || || ||||| |||||||||||||||||||| || |||||||| ||| |||| |
gtctgcataatatcatacggccccttcttttaaataaagaattacattatttttggatattgtccttcatcttcaatcgtgtagttctgaaaaaatgtacaaatagagtgaagtgaggctaatcctacaatgcgattgtagATCGGAGGAACTAGTGAAGTGGAAGTCAATGAGAAAAAAGATCGTGTAACGGATGCCTTGAATGCCACTAAAGCAGCTGTGGAAGAGGGCATTGTACCCG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
--------------------------gttagtccatgttataatg----ttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctg---gagctaatt---------gtgttta--gATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
                          |||    | | | | ||||    || | ||     || |||  |  | |     ||  |||  |     | ||| || |    ||  | |||         ||| |||  |||||||||||| ||||||| ||| ||| |||||||||||||| | || || ||||| ||||||||||| ||||| || ||||| ||||| ||| | || |
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------gttagtccatgttataatgttttgggagtcttagaat-catagcagcctggttgtaagtgtc-ttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
                            |  |  |  |  |||||  || | |     ||  | ||   | |  | ||| | | | || |||  ||   || |||   |   |   | ||||| |||||||| |||||||  || ||    |||||||||||| | || || ||||| ||||| ||||||||||| || ||||| ||||||||| | || |
gtatatccatgtacttcaattatctgtctcatttac-tcgtaatggatttgcatctgcagtttgcagtcctgattcgttattattttcgttgaaattgattttggttttttataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG

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|124764522|gb|EH854652.1|EH854652
EST:     CTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAG                         ATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAAGACAGAGTGAC
genomic: CTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGgttagtccat ... ttgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAA-GACAGAGTGAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
                       ttgttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG