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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcttcctttctcgtttctctctgtcacaagcatgagatagttgcaatttggtggtgttatctaatgggaataagctctctaacttgatcttattttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT

Basic information

species Arabidopsis thaliana
transcript AT4G29040.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------tgtcttcctttctc-gtttctctctgtcacaagcatgagatagttgcaatttggtggtgttatctaatgggaataagctctctaact---tgatcttatttt---agGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT
                                                                                | | | ||||| ||  | | | ||||    | |||| |  |  ||  | | |   | | | |  ||    | |   |  |  | |||   |||   | |||    |||| ||||| ||||||||||| || ||||||||| | ||||| |||||||| || ||||| |||||  | || |||||||| ||||| || |||||| | |
gtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------tgtcttcctttctcgtttctctctgtcacaagcatgagatagttgcaatttggtggtgttatcta--atgggaataagctctc-taacttgatcttattt-tagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT
                                                                  ||   ||     | || | | | | ||  ||  |     |  ||  | |||   | | | |  ||  |||    |  |   |  | ||||||   | | |  |||| || || || |||||||| || ||||||||| | |||||||||||||| || ||||| |||||  | || |||||||| || || ||  ||||| | |
gtcagtattctgtcttgcaagtatacaagatgtcaatatattgcttagtattgcaggggcaggctttgatatctgcctttgtctatgtttatccaaattacactctttttctacttttcagttttcaaatagcatgtacttgggtagtgattacttgaaactgtctgcagGCTGTGGCTAACTCAACATCTGCGACTTTCTTGCGTGTTGTTGGTAGTGAACTCATTCAAAAGTACCTTGGGGATGGTCCCAAACTAGTCCGAGAATTGT

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 2
---------------------------tgtcttcctttctcgtttctctctgtcacaagcatgagatagttgcaatttggtggtgtt---atctaatgggaata--agctctcta--acttgatcttat-----tttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT
                              ||   ||  | |  | ||    || |     |   ||  ||    |||||  |||||   || ||| | |  |   |||    ||  |||    ||| |     || |||| || || || ||||||||||| || |||||| | |||||||||||||| ||||| || ||||| ||||||||||| || || ||||| ||||||||||
gtttgtgtttatcttttgcttcttctagagctgttttaatagagtttcaacatctcctttttactatctttatcttttggcagtgtttcaatttaaggagtgtttcagcatcttaagactatgccttttgtgtattcagGCTGTGGCAAACTCAACATCAGCAACATTCTTGCGTGTTGTTGGTAGTGAACTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTAAGAGAACTTT

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 2
--------------------------tgtcttcctttctcgtttctctctgtcacaagcatgagatagttgcaatttggtggtgtt---atctaatgggaat--aagctctctaacttgat----cttat---tttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT
                             ||   ||  | |  | ||    || |     |   |   ||    || ||  |||||   || ||| | |  |   |||    |||    ||     || |   || |||| || || || ||||||||||| || |||||| | ||||||||||||||  |||| || ||||| ||||||||||| || || ||||||||||||||||
gtttgcatttatctttgcttcttctagagctgttttaatagagtttcagcatctcctttttactacctttatctttaggcagtgttttgatttaaggagtgttccagcatcttaagacaatgccttttgtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAATTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTGAGAGAACTTT

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
------tgtcttcctttctcgtttctctctgtcacaagcatgagatagttgcaatttggtggtgttatctaatgggaataagctctctaacttgatcttattttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT
        |||  || | ||   | | | | | |  |   ||       | | |       |    ||| | |  |  |||    |  ||     | |  ||| |||| || || || ||||||||||| || || ||| | ||||||||||||||  | || || || || |||||||||||||| |||||||| || |||||||
gatccacatctcactgtgtcaactttgttt-ttattattgtgtatcgtgtactacaca-cagcacaatcaatttagtctaa----tacaaacccttttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 2
tgtcttcctttctcgtttctctctgtcacaagcatgagatagttgcaatttggtggtgttatctaatgggaat------aagctctctaacttgatct-tat-tttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT
       |||| |  |||   | | | | |  | ||   |||||| |  |  | |  | |  ||  |   | |      || ||  | | | | || | | |  | |||| ||||| || || |||||||| ||||||||  | |||||||| |||||| | ||||| || |||||||||||||| || ||  | ||||| ||  | |
-------ctttgttatttacttttcttatattcttgtt-tagttgaagatcagagtagcttccttgtcaaagttgttctaaacttgcaaccctcatttatgtactcagGCAGTTGCAAACTCTACATCAGCAACTTTCTTACGTGTTGTTGGCAGTGAGTTAATTCAAAAATATTTGGGAGATGGGCCAAAATTAGTGAGGGAGTTAT

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 2
tgtcttcctttctcgtttctctctgtcacaagcatgagatagttgcaatttggtggtgttatctaatgggaataagctctctaacttgatcttattttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT
                             |||  ||| ||        |||   |||| |   |  |   ||  | ||  ||   ||| |  ||    |||| ||||| || || ||||| || || |||||| | |||||||| || ||||| ||||| |||||||||||||| |||||||||||||| || || || |
---------------------------gtaagtgtgacatc-------ttttaaggtgctgcttcgt---aactaactagct---ttggttctac---agGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 2
tgtcttcctttctcgtttctctctgtcacaagcatgagatagttgcaatttggtggtgttatctaatgggaataagctctctaacttgatcttattttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT
                             ||   ||| ||        ||||  |||| ||  |  |   ||| | ||  ||   ||| |  ||    |||| ||||| || || ||||| || || |||||| | |||||||| || ||||| ||||| |||||||||||||| |||||||||||||| || || || |
---------------------------gtaaatgtgacatc-------tttgaaggtgctacttcgt---aattaactagct---ttggttctac---agGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT

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|125066726|gb|EL133492.1|EL133492
EST:     ACATTGCTTGCTAAG                         GCGGTTGCGAATCCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAG
genomic: ACATTGCTTGCTAAGgtttgtcttt ... cttattttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAG
EST: gi|164113956|gb|ES101350.1|ES101350
EST:     CCTGGAACTGGGAAGACTTTGCTTGCTAAG                         GCGGTTGCGAATTCTACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAG
genomic: CCTGGAACTGGGAAGACATTGCTTGCTAAGgtttgtcttt ... cttattttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAG
EST: gi|125016779|gb|EL089048.1|EL089048
EST:     TGGGAAGACATTGCTTGCTAAG                         GCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAG
genomic: TGGGAAGACATTGCTTGCTAAGgtttgtcttt ... cttattttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAG
EST: gi|47831321|gb|CK121005.1|CK121005
EST:     GTGTGATTTTGTATGGTGAGCCTGGAACTGGGGAGACTTTGCTTGCTAAG                         GCGGTTGCGAATTCTACATCAG
genomic: GTGTAATTTTGTATGGTGAGCCTGGAACTGGGAAGACATTGCTTGCTAAGgtttgtcttt ... cttattttagGCGGTTGCGAATTCAACATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttggtggtgttatctaatgggaataagctctctaacttgatcttattttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT
                                            tcttatttt  CT-rich tract
                                        ttgatcttatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcttcctttctcgtttctctctgtcacaagcatgagatagttgcaatttggtggtgttatctaatgggaataagctctctaacttgatcttattttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - cctttct
- - - - - - - - -tctctct
- - - - - - - - - - - - - -acaagca
- - - - - - - - - - - - - - - - - - - - - - - aatttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaataag