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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggatggtgcttcttctgacatgagccaccattccataagcccaaaagaaccttggtgttccccttctcataggacagtgtggttttctgttttcttagGTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGTCATGGCCCATTGCTATGCAAGGTAGGGACATAGTAGCCATTGCTAAAACTGGCT

Basic information

species Arabidopsis thaliana
transcript AT3G01540.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G066440_T01 (Zea mays), 3'ss of exon 5
-------ggggatggtgcttcttctgacatgagccaccattccataagcccaaaaga-accttggtgttccccttctcataggacagtgtggttttctgttttcttagGTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGTCATGGCCCATTGCTATGCAAGGTAGGGACATAGTAGCCATTGCTAAAACTGGCT
          | || |      | |   ||||       ||| | |  |  | |  | |    | |  | | | ||||  | |       | | |     |||   |||| ||    ||||| |||||||| |||||||| || ||||||||||||||||| ||||||||| | |||||||| ||||||||  | || || || || |
gccttttctcgttgctatagactatagtatgaatt-ttgttctaaacacagatataatattcagataatactcatctctgaag-------gatatctaccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT

upper sequence: AT3G01540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G08750.1 (Glycine max), 3'ss of exon 8
--------------ggggatggtgcttcttctgacatgagccaccattccataagcccaaaagaaccttggtgttccccttctcataggacagtgtggttttctgttttcttagGTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGTCATGGCCCATTGCTATGCAAGGTAGGGACATAGTAGCCATTGCTAAAACTGGCT
               ||||   ||||||||| | ||| | |  |   || ||||| || ||||||      | | |                    | |||||   ||| ||||||||  | ||| || ||||| || |||||||||||||| || |||||||||||||||||| | |||||||| || ||||| |||||||||||||| ||||
gtggcttgcatatgagggacaatgcttcttccggcattaactcc---tctataagtcccaaagaaaaccaatctcctg------------------gattttcc--ttttttagGTACAAAATGCTGGGTTCTCAGCCCCAACTCCAATTCAGGCACAGTCATGGCCCATTGCTCTTCAAGGTAGAGATATAGTTGCCATTGCTAAAACAGGCT

upper sequence: AT3G01540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 4
-----------------------ggggatggtgcttcttctgacatgagccaccattccataagcccaaaagaaccttggtgttccccttctcataggacagtgtggttttctgttttcttagGTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGTCATGGCCCATTGCTATGCAAGGTAGGGACATAGTAGCCATTGCTAAAACTGGCT
                        |||||| ||||||||| ||||| | |  |   || ||||| || ||||||      | | |                    | |||||   ||| ||||||||  | ||| || ||||| || |||||||||||||| || |||||||||||||||||| | |||||||| || ||||| |||||||||||||| ||||
caagcattggtggcttgcatatgagggatgatgcttcttccgacattaactcc---tctataagtcccaaagaaaaccaatctcctg------------------gattttcc--ttttttagGTACAAAATGCTGGGTTCTCAGCCCCAACTCCAATTCAGGCACAGTCATGGCCCATTGCTCTTCAAGGTAGAGATATAGTTGCCATTGCTAAAACAGGCT

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|164084671|gb|ES141651.1|ES141651
EST:     CTCTAATG-CCTTTGAAGCTACTGGTTTTCCACCTGAGCTTCCGCGGGAG                         GTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGT
genomic: CTCTAATGTCCTTTGAAGCTACTGGTTTTCCACCTGAGCTTCTGCGGGAGgtatgattgg ... gttttcttagGTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGT
EST: gi|125320386|gb|EL334471.1|EL334471
EST:     CTCTAATGTCCTTTGAAGCTACTGGTTTTCCACCTGAGCTTCTGCGGGAG                         GTACTACAGTGCAGGTTTCTCTGCTCCAACT
genomic: CTCTAATGTCCTTTGAAGCTACTGGTTTTCCACCTGAGCTTCTGCGGGAGgtatgattgg ... gttttcttagGTACT-CAGTGCAGGTTTCTCTGCTCCAACT
EST: gi|124984002|gb|EL056695.1|EL056695
EST:     TGAAGCTACTGGTTTTCCACCTGAGCTTCTGCGGGAG                         GTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAA
genomic: TGAAGCTACTGGTTTTCCACCTGAGCTTCTGCGGGAGgtatgattgg ... gttttcttagGTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAA
EST: gi|116438332|gb|EG480924.1|EG480924
EST:     CTCTAATGTCCTTTGAAGCTACTGGTTTTCCACCTGAGCTTCTGCGGGAG                         GTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGTCATGG
genomic: CTCTAATGTCCTTTGAAGCTACTGGTTTTCCACCTGAGCTTCTGCGGGAGgtatgattgg ... gttttcttagGTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGTCATGG
EST: gi|164231619|gb|EL995166.1|EL995166
EST:     GGTTTTCCACCTGAGCTTCTGCGGGAG                         GTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGTCATGG
genomic: GGTTTTCCACCTGAGCTTCTGCGGGAGgtatgattgg ... gttttcttagGTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGTCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagaaccttggtgttccccttctcataggacagtgtggttttctgttttcttagGTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGTCATGGCCCATTGCTATGCAAGGTAGGGACATAGTAGCCATTGCTAAAACTGGCT
                                       ttttctgttttctt  CT-rich tract
                                              ttttctta  TA-rich tract