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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccccctccctccttcctttaagtttagtttaacatgttcctccaagttgaatcattttttgtatgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCCGAGATGGTCAGGGACTTCTTTTGGGATGATGAGTTCCGTTCCAAGTGGG

Basic information

species Arabidopsis thaliana
transcript AT1G64720.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G36050.2 (Glycine max), 3'ss of exon 2
gtacccccctccctccttcctttaagtttagtttaacatgttcctccaagttgaatcattttttgtatgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCCGAGATGGTCAGGGACTTCTTTTGGGATGATGAGTTCCGTTCCAAGTGGG---------------
|||| ||   || | | | |||    |||     |   ||||         ||| | |   | | |    ||  ||| ||| || || |||||||| |||||||| ||||| || || || | ||| ||| |||| ||||| ||||||||||||||||||||| | |  |||||||               
gtacgccttacctttcattcttcccttttg---cagtttgttagaattgagtgagtgagggtgtatgct-tgttagagtggaccgccgcagTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCTGAGTTGGTGAGGGATTTCTTTTGGGATGATGAGTTCAGGTTGAAGTGGGATGACATGCTTATAC

upper sequence: AT1G64720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G36050.1 (Glycine max), 3'ss of exon 2
gtacccccctccctccttcctttaagtttagtttaacatgttcctccaagttgaatcattttttgtatgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCCGAGATGGTCAGGGACTTCTTTTGGGATGATGAGTTCCGTTCCAAGTGGG
|||| ||   || | | | |||    |||     |   ||||         ||| | |   | | |    ||  ||| ||| || || |||||||| |||||||| ||||| || || || | ||| ||| |||| ||||| ||||||||||||||||||||| | |  |||||||
gtacgccttacctttcattcttcccttttg---cagtttgttagaattgagtgagtgagggtgtatgct-tgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCTGAGTTGGTGAGGGATTTCTTTTGGGATGATGAGTTCAGGTTGAAGTGGG

upper sequence: AT1G64720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0025g02820.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------------------------------------------gtacccccctccctccttcctttaagtttagtttaacatgttcctcca--agttgaatcattttttgtatgat--gccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCCGAGATGGTCAGGGACTTCTTTTGGGATGATGAGTTCCGTTCCAAGTGGG
                                                                                                   |  |   |     |   | |    |||| | ||| | || ||   | |    |||| | |  || |||  | |  || ||| ||| ||||| || || |||||||| ||| | ||||||||||| ||||| ||| |||| ||||| ||||||||||||||||  ||  | |  |||||||
gtaggctttctttctcttagtattttctcttaggcatttggtggaataagaataaatgaattagcacccagaagttagcacatatgattcttccttctagggcttgctctattttatacaaatagttaaatttcatatcttgtgcgattgattgagttaaattctgttgggtttgctagACTGGCCCTCCACAATATCGTAGCAGTACTATCTTTGAGGATGCTACTCCTGAGTTGGTGAGGGATTTCTTTTGGGATGATGGCTTTAGATTGAAGTGGG

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|124998663|gb|EL070932.1|EL070932
EST:     GAGGCGAGATCCTGAG                         AATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
genomic: GAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
EST: gi|124706718|gb|EH798120.1|EH798120
EST:     CCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAG                         AATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAAGGATGCCACTCC
genomic: CCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGA-GGATGCCACTCC
EST: gi|86041615|gb|DR337370.1|DR337370
EST:     ACCGNTCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAG                         AATGGGGCTCCCCAGTACCGTAG
genomic: ACCGATCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAG
EST: gi|86041616|gb|DR337371.1|DR337371
EST:     ACCGATCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAG                         AATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
genomic: ACCGATCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
EST: gi|116456484|gb|EG499076.1|EG499076
EST:     ACCGATCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAG                         AATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
genomic: ACCGATCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
EST: gi|124730101|gb|EH821503.1|EH821503
EST:     CCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAG                         AATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
genomic: CCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
EST: gi|124791788|gb|EH881467.1|EH881467
EST:     TATCAAGCTTGGAGGCGAGATCCTGAG                         AATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
genomic: TATCAAGCTTGGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
EST: gi|86041612|gb|DR337367.1|DR337367
EST:     ACCGATCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAG                         AATGGGC-TCCC-AGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
genomic: ACCGATCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
EST: gi|125216642|gb|EL230725.1|EL230725
EST:     GGAGGCGAGATCCTGAG                         AATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
genomic: GGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
EST: gi|124727722|gb|EH819124.1|EH819124
EST:     ATCAACCCCAACCTTCTCATATCAAGCTTTGGAGGCGAGATCCTGAG                         AATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
genomic: ATCAACCCCAACCTTCTCATATCAAGC-TTGGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCC
EST: gi|125048954|gb|EL121223.1|EL121223
EST:     AACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAG                         AATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTT
genomic: AACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTT
EST: gi|86041617|gb|DR337372.1|DR337372
EST:     ACCGATCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAG                         AWTGGGCCTCCCCAGTACCGTAGCAGAACTGT
genomic: ACCGATCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGT
EST: gi|86041611|gb|DR337366.1|DR337366
EST:     ACCGATCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATC-TGAG                         AATGGGC-TCCC-AGTA
genomic: ACCGATCAACCCCAACCTTCTCATATCAAGCTTGGAGGCGAGATCCTGAGgtacccccct ... atgatgccagAATGGGCCTCCCCAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagtttagtttaacatgttcctccaagttgaatcattttttgtatgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCCGAGATGGTCAGGGACTTCTTTTGGGATGATGAGTTCCGTTCCAAGTGGG
         gtttaac  putative branch site (score: 3)
                                aatcattttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccccctccctccttcctttaagtttagtttaacatgttcctccaagttgaatcattttttgtatgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCCGAGATGGTCAGGGACTTCTTTTGGGATGATGAGTTCCGTTCCAAGTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG