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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaattaatcgattcagatactaatgcttttcgatttaggtttttttgaatcgaagcttgagcttgatttgtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG

Basic information

species Arabidopsis thaliana
transcript AT3G25230.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------gtaattaattaatcgattcagatactaatgcttttcgatttaggtttttttgaatcgaagcttgagcttgatttgtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG
                                               |   ||  ||  |   ||       |  |  ||| | ||   |   || ||| || ||   ||||| ||   ||| || | |||| ||||||||||| |||||||||||||| ||  |||| ||||| || |||||||| |  || || ||||| ||||| ||||| ||||
gtactcatcccccgatcacccatttctcaactgtatcaattctttttgcttttttttttttcttttcttcttttcttttttactatgctgcaattattggattgat-tttgagtttttgttgatttt-cagTTCATTACACTGGGACTTTGCTTGATGGAACTCAGTTCGATTCCAGCCGTGATAGGGGGACTCCGTTCAAGTTCACCCTTGGCCAAG

upper sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv00s0260g00070.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------------gtaattaattaatcgattcagatactaatgcttttcgatttaggtttttttgaatcga-agcttgagcttga---tttgtt--tctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG
                                       |  ||  ||  |   ||       |  | ||||||  |||   | |  |  |||     | ||||  ||||   ||||||  | | |||| ||||||||||| |||||||||||||| ||  |||| ||||| || |||||||| |  || || ||||| ||||| ||||| ||||
gtactcatcccccgatcacccatttctcaactgtatcaattcttttttctttttttttttcttttcttcttttcttttttactatgctgcaattattggattgattttgagtttttgttgattttcagTTCATTACACTGGGACTTTGCTTGATGGAACTCAGTTCGATTCCAGCCGTGATAGGGGGACTCCGTTCAAGTTCACCCTTGGCCAAG

upper sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S109_70V6.1 (Physcomitrella patens), 3'ss of exon 2
--gtaattaattaatcgat----tcagatact---aatgcttttcga--tttaggttttt---ttgaatcgaagcttgagcttgatt--tgtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG
  |||   |||    | |     || || | |   | ||| |  ||   ||   |||  |   | | ||| ||| |    || | ||  | ||  | |||||||||||||||| ||| | || |||||||||||||||||||| ||||  || ||||    ||||||||  ||||   | || ||||
gtgtagccaatctgactacactctcggacattttgactgcctagcggagttctagttcctaaatggcatctaagttctgtctcggttactcttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG

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|164180836|gb|ES049458.1|ES049458
EST:     TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAG                         TGCATTACACT
genomic: TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAGgtaattaatt ... gtttctgcagTGCATTACACT
EST: gi|86070352|gb|DR366109.1|DR366109
EST:     TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAG                         TGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
genomic: TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAGgtaattaatt ... gtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
EST: gi|86070353|gb|DR366110.1|DR366110
EST:     TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAG                         TGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGNG
genomic: TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAGgtaattaatt ... gtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
EST: gi|301501375|gb|HO206915.1|HO206915
EST:     TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAG                         TGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
genomic: TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAGgtaattaatt ... gtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
EST: gi|116475203|gb|EG517795.1|EG517795
EST:     TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAG                         TGCATTACACTGGAACTTTGCTTGATGGGACGAGGTTTGATTCGAGTCGTG
genomic: TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAGgtaattaatt ... gtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
EST: gi|116434999|gb|EG477591.1|EG477591
EST:     TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAG                         TGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
genomic: TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAGgtaattaatt ... gtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
EST: gi|116475202|gb|EG517794.1|EG517794
EST:     TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAG                         TGCATTACACTGGAACTTTGCTTGATGGGACGAGGTTTGATTCGAGTCGTG
genomic: TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAGgtaattaatt ... gtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
EST: gi|116435001|gb|EG477593.1|EG477593
EST:     TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAG                         TGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
genomic: TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAGgtaattaatt ... gtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
EST: gi|86070354|gb|DR366111.1|DR366111
EST:     TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAG                         TGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG
genomic: TAAAGAAGGTGAAGGATATGAAACTCCTGAGAATGGCGATGAAGTTGAAGgtaattaatt ... gtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttcgatttaggtttttttgaatcgaagcttgagcttgatttgtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG
                                    gcttgat  putative branch site (score: 5)
                                          tttgtttct  CT-rich tract
        atttaggttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaattaatcgattcagatactaatgcttttcgatttaggtttttttgaatcgaagcttgagcttgatttgtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG

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