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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG

Basic information

species Arabidopsis thaliana
transcript AT2G44120.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 4
gtaggtttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttg--------tgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG
                                                                                                | |  | |  | || ||||   ||| |   |   ||| ||||||   |  |    |||  || ||    | |||        | ||||||||||||||||| || || ||||| |||||||||||  | |||||||||||| | ||||| ||||| ||  | || ||
----------------------------------------------------------------------------------------------gttggtttatgaaccagttttcttagaaatgcgtgaactcttgcgtacgctggtgtattaactttgtgcttaattgtttgattctacagATCTTCAATGGTGTCTTCCTCAAGGTTAACAAGGCAACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G178807_T03 (Zea mays), 3'ss of exon 3
gtaggtttcacagtttgttattttcatccagctatattagcctaacata-tgattattgattaatatttgttatatgttcaaactaatatgtgatagttgc-ctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG
                                  |||    ||  |  | || ||  |||||   | ||| |||          | |    ||  |  ||  ||||  |  ||   |   |   |    |||||    ||    ||  | || |  | | |||     ||   |||||||||||||||||| ||||| ||||| |||||||||||  |                                       
---------------------------------gtatggctctgtcccaatggttgctgatt--cagttgctatgctcaagtgttgactgttgtcaaatgtgctgtgtagTATCAATGCCATGCACCCCAAGACC--CGCAAGATCTTGCAGCT--CCTGCGT-----TTGAGGCAGATCTTCAATGGTGTCTTTCTCAAGGTTAACAAGGCAACTATT--------------------------------------

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G23750.2 (Glycine max), 3'ss of exon 4
gtaggtttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG
                                                                |||| ||     | ||||        | |||  ||  | ||  |    |||  |      |||||| | |||  ||  |   ||   |||  ||  | || |      ||||| ||||||||||| ||||| || || ||||| || ||||| |||||||||| | ||||||| || || |||||||| ||
----------------------------------------------------------------attt-ttgagcatgcaaagagcaccattata-ctgaatatttgta---tttgtattcatatagaag-caatttggtgatgctgatccttatctttttgtaaa-----acagATTTTCAATGGTGTATTTCTCAAAGTTAACAAAGCCACAGTGAACATGCTGCACAGAGTTGAGCCCTATGTGACTTATGG

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G02270.1 (Glycine max), 3'ss of exon 4
gtaggtttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG
                                                                 |||     |||  || |  ||  | | ||| |    ||||  |  || ||   | | |  | |  | | |   | ||    ||   |||  ||  | || |      ||||| ||||||||||| ||||| || || ||||| || ||||| |||||||||| | ||||||| || || |||||||| ||
-----------------------------------------------------------------tttagaggatg--cagaggaaactattatactcaa-tgtttgtatttgttttcatataaaaaagcaatttgatgatgct--gatccttatctttttgtaaa-----acagATTTTCAATGGTGTATTTCTCAAAGTTAACAAAGCCACAGTGAACATGCTGCACAGAGTTGAGCCGTATGTGACTTATGG

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 2
gtaggtttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG
                                                                  || | ||  | |   |||||| |  |  || |  |            ||| || |  | ||    || |   |   | ||||  ||  | |||   |   |   | ||||| |||||||| ||||||||||| |||||||| |||||| | |||||| ||| | | ||||| || || |||||||| ||
---------------------------------------------------------------ctcttatcatgagctt--actaatctaagcaagctatcc---------cattagaaaaatggagtgttctttgatgacat-aagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACATGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s1526g00010.t01 (Vitis vinifera), 3'ss of exon 3
gtaggtttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG
                                                                                                                                                ||||  ||  | |||   |   |   | ||||| |||||||| ||||||||||| |||||||| |||||| | |||||| ||| | | |||                    
------------------------------------------------------------------------------------------------------------------------------------------------aagatcttctcattcacttctttgaatacagATGTTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACATGTTGCACAGGGTT--------------------

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 3
gtaggtttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG
                                                                  || | ||  | |   |||||| |  |  || |  |            ||| || |  | ||    || |   |   | ||||  ||  | |||   |   |   | ||||| |||||||| ||||||||||| |||||||| |||||| | |||| | ||| | | ||||| || || |||||||| ||
---------------------------------------------------------------ctcttatcatgagctt--actaatctaagcaagctatcc---------cattagaaaaatggagtgttctttgatgacat-aagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 3
gtaggtttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG
                                                                  || | ||  | |   |||||| |  |  || |  |            ||| || |  | ||    || |   | | | |||   ||  | |||   |   |   | ||||| |||||||| ||||||||||| |||||||| |||||| | |||||| ||| | | ||||| || || |||||||| ||
---------------------------------------------------------------ctcttatcatgagctt--actaatctaagcaagctatcc---------cattagaaaaatggagtgttctttgatgatat-aaggtcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACATGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0054g00210.t01 (Vitis vinifera), 3'ss of exon 4
gtaggtttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG
                                                                  || | ||  | |   |||||| |  |  || |  |            |||||| |  | ||    || |   |   | ||||  ||  | ||||  |   |   | ||||| |||||||| ||||||||||| |||||||| |||||| | |||||| ||| | | | ||| || |  |||||||| ||
---------------------------------------------------------------ctcttatgatgagctt--actaatctaagcaagctatcc---------cattaaaaaaatggagtgttctttgatgacat-aagatcttctcattcgcttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACATGTTGCACAGGGATGAGCCTTGTGTGACTTATGG

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|86036885|gb|DR332640.1|DR332640
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGNGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|125324014|gb|EL338094.1|EL338094
EST:     ATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: ATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|86036872|gb|DR332627.1|DR332627
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|164121522|gb|ES012486.1|ES012486
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTG
EST: gi|86036886|gb|DR332641.1|DR332641
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|86036883|gb|DR332638.1|DR332638
EST:     CATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT-GAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|86036875|gb|DR332630.1|DR332630
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAA
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAA
EST: gi|86036881|gb|DR332636.1|DR332636
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|86036876|gb|DR332631.1|DR332631
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|164149096|gb|EL967429.1|EL967429
EST:     GCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: GCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|164097943|gb|ES159694.1|ES159694
EST:     GCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: GCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|86036880|gb|DR332635.1|DR332635
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|86036879|gb|DR332634.1|DR332634
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|86036882|gb|DR332637.1|DR332637
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|86036873|gb|DR332628.1|DR332628
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|86036877|gb|DR332632.1|DR332632
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|86036878|gb|DR332633.1|DR332633
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
EST: gi|86036874|gb|DR332629.1|DR332629
EST:     CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG                         ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG
genomic: CCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggtttca ... atttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG
                                        tatacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC