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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctctctctgacttcaccaatattcgtgttcctatcaagatactgtatatgcaacaataattactcacaacaatttattgtgttgtgtgtttgtagCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGCGCATACGATACAAGGAACATCTTCCAGTCGCTTGACTTGGCATGGACAC

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G181151_T04 (Zea mays), 3'ss of exon 5
----------------gtacctctctctga-cttcaccaatattcgtgttcctatcaagatactgtatatgcaacaataattactcaca-----acaatttattgtgttgtgtgtttgt----agCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGCGCATACGATACAAGGAACATCTTCCAGTCGCTTGACTTGGCATGGACAC
                 ||  |  ||  |  |||   |    | ||||      | |    ||      |     | |  ||  ||| |     | ||  || |||  |||   ||  |    |||| || |||||||| || || || ||||| |||||||||||||  ||||| |||||||| ||| |||||||||||||||| || ||  | ||||||||| 
gtctgtttcgagtgaaataaattcctaagggcttgttcgggttgcgtgcagacgtaaccgaacaagccctaagttagttctttttcagatgtccaaaacctaatgttctgttacttcttgctcagCTTTACTTAGAGTTCCTTGACAAGTTTGAGAGGAAGTTTGTGACACAAGGAGCATACGACACACGGAACATCTTCCAGTCACTAGATCTTGCATGGACAT

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 13
gtacctctctctgacttcaccaatattcgtgttcctatcaagatactgtatatgcaacaataattactcacaacaatttattgtgttgtgtgtt-tgtagCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGCGCATACGATACAAGGAACATCTTCCAGTCGCTTGACTTGGCATGGACAC
         ||||     |   | ||     ||| ||   || || |   | | ||          | || |||    | || ||||   | ||    |||| || |||||||| || || || ||||| |||||||||||||  ||||| ||||| || ||| |||||||||||||||| || ||  | ||||||||| 
--------gtctgttgcgagtgaaat--aaattcgta---agttagttctttttcaga------cccccaaaacttaatgttctgttccttattgcacagCTTTACTTAGAGTTCCTTGACAAGTTTGAGAGGAAGTTTGTGACACAAGGAGCATATGACACACGGAACATCTTCCAGTCACTCGATCTTGCATGGACAT
















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|116471554|gb|EG514146.1|EG514146
EST:     AAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG                         CTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAGGGC
genomic: AAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTGgtacctctct ... gtgtttgtagCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGC
EST: gi|86084595|gb|DR380354.1|DR380354
EST:     AAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG                         CTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGC
genomic: AAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTGgtacctctct ... gtgtttgtagCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGC
EST: gi|116428286|gb|EG470878.1|EG470878
EST:     AAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG                         CTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGC
genomic: AAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTGgtacctctct ... gtgtttgtagCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGC
EST: gi|124784864|gb|EH874549.1|EH874549
EST:     AAGAAGCTCTGTCTTCCGAGGATCTG                         CTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAAGG
genomic: AAGAAGCTCTGTCTTCCGAGGATCTGgtacctctct ... gtgtttgtagCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAA-GG
EST: gi|164066061|gb|ES038801.1|ES038801
EST:     AAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG                         CTGTATTTAGAGTTTCTGGATAAATTTG
genomic: AAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTGgtacctctct ... gtgtttgtagCTGTATTTAGAGTTTCTGGATAAATTTG
EST: gi|116428287|gb|EG470879.1|EG470879
EST:     AAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG                         CTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGC
genomic: AAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTGgtacctctct ... gtgtttgtagCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGC
EST: gi|125310674|gb|EL324759.1|EL324759
EST:     TCTTCCGAGGATCTG                         CTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGC
genomic: TCTTCCGAGGATCTGgtacctctct ... gtgtttgtagCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGC
EST: gi|124758740|gb|EH848870.1|EH848870
EST:     CTTCCGAGGATCTG                         CTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGC
genomic: CTTCCGAGGATCTGgtacctctct ... gtgtttgtagCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtatatgcaacaataattactcacaacaatttattgtgttgtgtgtttgtagCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGCGCATACGATACAAGGAACATCTTCCAGTCGCTTGACTTGGCATGGACAC
                    tactcac  putative branch site (score: 1)
           aacaataatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctctctctgacttcaccaatattcgtgttcctatcaagatactgtatatgcaacaataattactcacaacaatttattgtgttgtgtgtttgtagCTGTATTTAGAGTTTCTGGATAAATTTGAAAGGAAGTTTGTGATGCAAGGCGCATACGATACAAGGAACATCTTCCAGTCGCTTGACTTGGCATGGACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA