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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagactaaatcctgctggacaccacaaaactatataatctccttggctgatttggaattttctaactcaaattctacaaaacactttttttccatttgttaagTTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAAATGTTTCACTGCCAAATGGAAGAGCACTGCCTCCATTGTTTAACTTCACTGCCC

Basic information

species Arabidopsis thaliana
transcript AT4G00720.1
intron # 11
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 11
lower sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 11
----------------------------------------------------------------------------------------gtaagactaaatcctg-ctggacaccacaaaactatataatctc----cttggctgatttggaattttctaactcaaattctacaaaacactttttttccatttgtta-agTTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAAATGTTTCACTGCCAAATGGAAGAGCACTGCCTCCATTGTTTAACTTCACTGCCC
                                                                                         | | ||| |    |  |        ||| |  |  ||| | |      | ||  ||| |  ||||||||      | ||||      |   |  ||    | ||||  |||||||||| ||||||||||| |||||||||||  | || || |||||||  |   ||||||||||  || || ||||||||||||| ||||||||||| |
gtaagttttaattttcttctagaaatgtcaccttttgtagcttaattatatatgcagtcacactaatgaagatttatatgttgaaaaaattatacttagctttatccatgttttacatagtttcatattatagaagttaggaagatattcaattttctttggtta-ttctgttgtgctaatgattattttctgttgcagTTGGAAGCATGTGCACACCCTTTCTTTGATGATCTGCGAGAACCAAATGCATGCTTGCCAAATGGGCGACCATTGCCTCCATTGTTCAACTTCACTGCTC

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G45960.1 (Glycine max), 3'ss of exon 11
-----gtaagactaaatcctgctggacaccacaaaactatataatctccttggctgatttggaattttctaactcaaattctacaaaacactttttttccatttgttaagTTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAAATGTTTCACTGCCAAATGGAAGAGCACTGCCTCCATTGTTTAACTTCACTGCCC-
       | |  |  |  | | | || |  ||| ||      ||  |  |    ||  || |  | ||||        ||  || ||  | | |||     ||  | ||||||||||| ||||||||||| |||||||||||  | || || |||||||  |   ||||||||||   | || |||||||||||||  | |||||||| | 
tttacccatgcttgtacacagtttgatattacagaagctaggaagatattcaattgtctttggttattctg-------ttgcactaatgattattt----gttgttaaagtTGGAAGCATGTGCACACCCTTTCTTTGATGATCTGCGAGAACCAAATGCATGCTTGCCAAATGGGCAATCATTGCCTCCATTGTTCGATTTCACTGCTCA
















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|124819416|gb|EH904282.1|EH904282
EST:     ACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA                         TTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTA
genomic: ACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCAgtaagactaa ... atttgttaagTTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTA
EST: gi|125316190|gb|EL330275.1|EL330275
EST:     ACCTCGTCTCAAGACTCCTTCAGTATTCACCAAACCTTCGTTGCACTGCA                         TTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGG
genomic: ACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCAgtaagactaa ... atttgttaagTTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGG
EST: gi|125003466|gb|EL075735.1|EL075735
EST:     ACCTCGTCTCAAGA-TCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA                         TTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAA
genomic: ACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCAgtaagactaa ... atttgttaagTTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAA
EST: gi|124718430|gb|EH809832.1|EH809832
EST:     CCAAACCTTCGTTGCACTGCA                         TTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAAATGTT
genomic: CCAAACCTTCGTTGCACTGCAgtaagactaa ... atttgttaagTTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAAATGTT
EST: gi|124986600|gb|EL059109.1|EL059109
EST:     ACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA                         TTGGAAGCTTGTGACACACCCCTTCTTTGATGACTTACGGGATCCAA
genomic: ACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCAgtaagactaa ... atttgttaagTTGGAAGCTTGTG-CACACCCCTTCTTTGATGACTTACGGGATCCAA
EST: gi|164179714|gb|ES211638.1|ES211638
EST:     CCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCAACTGCA                         TTGGAAGCTTGTGCACACCCCTTCT
genomic: CCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCA-CTGCAgtaagactaa ... atttgttaagTTGGAAGCTTGTGCACACCCCTTCT
EST: gi|125076962|gb|EL139921.1|EL139921
EST:     GTTGCACTGCA                         TTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAAATGTT
genomic: GTTGCACTGCAgtaagactaa ... atttgttaagTTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAAATGTT
EST: gi|125297455|gb|EL311540.1|EL311540
EST:     GTACTCACCAAACCTTCGTTGCACTGCA                         TTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAAATGTT
genomic: GTACTCACCAAACCTTCGTTGCACTGCAgtaagactaa ... atttgttaagTTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAAATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttggaattttctaactcaaattctacaaaacactttttttccatttgttaagTTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAAATGTTTCACTGCCAAATGGAAGAGCACTGCCTCCATTGTTTAACTTCACTGCCC
           ttctaac  putative branch site (score: 1)
                                   ctttttttccatttgt  putative PPT
                             aaaacacttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagactaaatcctgctggacaccacaaaactatataatctccttggctgatttggaattttctaactcaaattctacaaaacactttttttccatttgttaagTTGGAAGCTTGTGCACACCCCTTCTTTGATGACTTACGGGATCCAAATGTTTCACTGCCAAATGGAAGAGCACTGCCTCCATTGTTTAACTTCACTGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA