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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttaacctgatccctcgtgttccttcatctctcttctatatttaatttactagtttactcatctgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG

Basic information

species Arabidopsis thaliana
transcript AT4G00720.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
-----------------------------------gtacttaacctgatccctcgtgttccttcatctctcttc--tatatttaatttactagttta----ctcatc-tgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
                                    |  || || | ||        || |   |  | | |||  | |  ||| ||    | | |      ||||  ||||| ||||  ||||| | || || || || |||||||||||| |||| |||||||| || ||||  || || ||||||||||| |||||||||||||| |||||||||
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctat-agATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
------------------------------------gtacttaacctgatccctcgtgttccttcatctctcttcta--tatttaatttactagttta----ctcatc-tgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
                                     |  ||  | | ||     |  || |   |  | | ||||   || ||| ||    | | |      | ||  ||||| ||||  || |  | || || || || |||||||||||| |||| |||||||| || ||||  || || ||||||||||| || ||||||||||| |||||||||
gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctat-agGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 9
---------------gtacttaacctgatccctcgt---gttcct-----tcatctctcttctatatttaatttactagtttactcatctgtacatctacc--agATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
                |  ||| |||  | | |  |   |||| |     |    ||   |   | ||  ||     | | |     |   ||  || ||   ||||  | || || || || ||||||||||||  ||| |||||||| |||||||| || || ||||||||||| || ||||| ||||| ||||| |||
gtaaagtttattgtgttctttatccttgtgctttataaggttcttgaaagttgcatcctgttggttttggatcattgaatctgagtgtaattatgtccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G45960.1 (Glycine max), 3'ss of exon 9
--------------------------gtacttaacctgatccctcgt-gttccttcatctctcttctatatt-taatttactagtttactcatc-tgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG-
                          ||  || |   | | | |    ||| | || | |   || |  ||| ||   |   ||| || | ||  ||| || |||  ||||  | || || || || ||||||||||||  ||| |||||||| |||||||| || || ||||||||||| || ||||| ||||| ||||| ||| 
taaagttaattgtgttctttatccttgtgttttataagcttcttgaaagttgcatcctattggttgtggattatagaatctgagtgtaattattatgtgca-ctat-agaTCTTGGGAACACCGACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAGG

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 9
----gtacttaacctgatccctcgtgttccttcatctctcttctatatt------taatttactagtttactcatctgtac-atctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
    |   | ||   | |     ||  | |    ||| |  |  |||||       |  | |  ||  |  |  |   |   || |   ||||||| || || || || |||||||||||   ||| |||||||| |||||||  |||||||||||||| ||||||||||||||||| |||||||||
gtttgctatcaagtggcttttctgttattcactttcttttcttaatattataggtcagctaagcaggatgttgttgcatgttatgtcttagATTCTGGGTACACCCACCAGAGAAGAAATTAAGTGCATGAATCCAAATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAG

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------------------------------------------------------------gtacttaac-ctgatccctcgtgttcct--tcatctctcttctatatttaatttactagtttact---catctgtacatc--taccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
                                                                                                           |||  |    ||    |   ||| |  |  | ||  ||   ||| | |  || |    |  |  |    |  ||    |   |   || |  | ||||| || ||| | || || |||  ||| ||||||||||| ||||| |||||||||||||||||||| || ||||| || |||||||||
gtagcttacatatggtagatgttgaggaagtgcaggggtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagttatgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttagGTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAG

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------gtacttaac--ctgatccctcgtgttccttcatctctcttcta-tatttaatttactagtttactcatctgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
                                         ||||||     ||| |      |||| |   |    | |  |  | |  | | ||     ||    |   ||   | |  ||| |  | ||||| || ||  | || || ||   ||| ||||||||||| ||||| |||||||||||||| |||||||| |||||||| |||||||| 
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgatgctgtggagtgtatgttattgaggaaaagttt-tgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------gtacttaac--ctgatccctcgtgttccttcatctctcttcta-tatttaattt-actagtttactcatctgtacatctac--cagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
                                         ||||||     ||| |      |||| |        | |  |  | |  | | | | ||  ||| | |   |||| | |    ||| |  | || || || ||  | || || |||  ||| ||||||||||| ||||| |||||||||||||| |||||||| ||||||||||||||||| 
gtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggggtgttatgatgctgtggagtgtgagtatgttattgaggagtacttgtgtggcagGTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAA

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------gtacttaacctgatccctcg-tgttccttcatctctcttctatatttaatttactagtttactcatc-tgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
                                                 ||        || |   | | |||    || | |   |  |  || | | |     ||| ||    | | | | | |  ||| || | ||||| || ||  | || || ||   ||| ||||||||||| |||||||||||||||||||| |||||||| || |||||||||||||| 
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------------------------------------------------------------gtacttaacctgatccctcg-tgttccttcatctctcttctatatttaatttactagtttactcatctgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
                                                                                                                  | |||    || |    || || |    ||    |  |   | |  |  |||  |||   |  ||    |  |  || || |  | ||||| |||||| | || || |||  ||| ||||||||||| ||||| |||||||||||||||||||| || ||||||||||||||||||
gtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatac-tgtagagcttatgagtaggcggatggtgatgttgac-agGTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAG

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
gtacttaacctgatccctcgtgttccttcatctctcttctatatttaatttactagtttactcatctgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
                    ||   | |  | | |    |||  |   |   |  | | |   |  || || |    ||| ||||||| || |||||  | || || ||   |||||||||||| || ||||| || |||||||| ||||||||||| || ||||| |||||||||
------------------gttggctcgttgtttttgccttatggtggctgggc--gctcataaagttggac-ttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 8
gtacttaacctgatccctcgtgttccttcatctctcttctatatttaatttactagtttactcatctgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
                    ||   | |  | | |    |||  |   |   |  | | |   |  || || |   | || ||||||| || |||||  | || || ||   |||||||||||| || ||||| || |||||||| ||||||||||| || || || |||||||||
------------------gttggctcgttgtttttgccttatggtggctgggc--gctcataaagttggacttgcgc-agGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAG

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|125134251|gb|EL175267.1|EL175267
EST:     TGGCATTGATCAGCTGGTGGAGATAATCAAG                         ATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTAC
genomic: TGGCATTGATCAGCTGGTGGAGATAATCAAGgtacttaacc ... catctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTAC
EST: gi|124729199|gb|EH820601.1|EH820601
EST:     CTGGTGGAGATAATCAAG                         ATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTAC
genomic: CTGGTGGAGATAATCAAGgtacttaacc ... catctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcatctctcttctatatttaatttactagtttactcatctgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG
                 atttaat  putative branch site (score: 4)
           ttctatatttaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttaacctgatccctcgtgttccttcatctctcttctatatttaatttactagtttactcatctgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA