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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttgagaatgtcatgtgagttcttgagaggaactaactatgtgaaaattttgttttaacttgttttctgttatacagCATTGAGGCAGCTTGTGCTGCGCATCCAACAGCGGATGTATTCATCAACTTTGCATCTTTTAGGAG

Basic information

species Arabidopsis thaliana
transcript AT5G49460.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 2
--------------gtaagttttgagaatgtcatgtgagttcttgaga---ggaactaactatgtgaaaattttgttttaacttgttttctgttatacagCATTGAGGCAGCTTGTGCTGCGCATCCAACAGCGGATGTATTCATCAACTTTGCATCTTTTAGGAG
               | | |    || |    |  | ||| | ||| |        |  || || |   ||||   |  |  |||| || | || | ||||||||| |||||||||||||| ||||| || || ||||| |||||||||||||| || ||||| ||
cttcagcatgccaattgaatacaaagtaaccaacttcagtgcatgacattctagtttttctgtggggtgatttgtctcaatgttgtcttattttttgcagCATTGAAGCAGCTTGTGCTGCACATCCTACTGCTGATGTCTTCATCAACTTTGCTTCATTTAGAAG

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G15020.1 (Glycine max), 3'ss of exon 3
--------------------------gtaagttttgagaatgtcatgtgagttcttgagaggaactaactatgtgaaaattttgttttaacttgttttctgttatacagCATTGAGGCAGCTTGTGCTGCGCATCCAACAGCGGATGTATTCATCAACTTTGCATCTTTTAGGAG
                            || ||| | | ||| ||| |  |||  |  ||||    |  | | |      | ||||   |||||||||        ||||||||| |||||||||||||| ||||| || || ||||| |||||||||||||| || ||||| ||
tttttcagctattgcatacaaagtaaccaactttagtgcatgacatttttgtttgtctgaggggtgatttgtcttggcgctatgtt--gacttgtttt-------gcagCATTGAAGCAGCTTGTGCTGCACATCCTACTGCTGATGTCTTCATCAACTTTGCTTCATTTAGAAG

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G04000.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------------------------gtaagttttgagaatgtcatgtgagttc----ttgagaggaactaactatg-----tgaaaattttgttt---taacttgttttctgtta--------tacagCATTGAGGCAGCTTGTGCTGCGCATCCAACAGCGGATGTATTCATCAACTTTGCATCTTTTAGGAG
                                                                                                  | | ||| | |    || |     |||    |  | || ||| |||| |      |||   | ||||||   |    || ||||||||         | |||| |||| |||||||||||||| ||||| || || ||||| |||||||||||||| || ||||| ||
gtatgtgttgctcattcatttctgtactcaaaatttcctttttctgcttcaatttggaatttggttgcttgaagttgaagccaaggggagatttttctttattttagtggtcttcttactttttcagaatacaaagtaaccaactttagtgcttgacgttcttgtttgtctggggtgatttctgttgacttattttgcagCGTTGAAGCAGCTTGTGCTGCACATCCTACTGCCGATGTCTTCATCAACTTTGCTTCATTTAGAAG

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G36840.1 (Glycine max), 3'ss of exon 4
gtaagttttgagaatgtcatgtgagttct--tgagaggaactaactat-------gtgaaaattt----tgttttaacttgttttctg------ttatacagCATTGAGGCAGCTTGTGCTGCGCATCCAACAGCGGATGTATTCATCAACTTTGCATCTTTTAGGAG
  | |       ||| | | || | || |  ||| ||||| |   | |       || ||| |||    |||| | |    | |  ||      || | ||| ||||| |||||||||||||| || || || || ||||| |||||||| |||||||| ||||| ||
--atgccactgaaatataaagtaacttgtaatgaaaggaaattcttgttttgtttgtcaaagtttaatgtgttcttagccatatgttgaattcttttttcagTATTGAAGCAGCTTGTGCTGCACACCCCACTGCTGATGTGTTCATCAATTTTGCATCATTTAGAAG

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S46_63V6.3 (Physcomitrella patens), 3'ss of exon 3
-------------gtaagttttgagaatgtcatgtgagt---tcttgagaggaactaactatgtgaaaattttgttttaacttgttttctgtta-tacagCATTGAGGCAGCTTGTGCTGCGCATCCAACAGCGGATGTATTCATCAACTTTGCATCTTTTAGGAG
             ||  || |||   ||| | |  ||     | || ||    ||  | |      | |   ||   |   ||    || |||  | |||||||    | || ||    |  |||||||| || ||||| ||||||||||||||||||||| | ||
aatttgaagctgagtttgtcttgtttatgactttcgaacaacttttaagtattacagaattatcatagaagctgacctgctttaccatcggtttctgcagCATTCCATCTGCGTGCAAAGTTCATCCAACGGCAGATGTTTTCATCAACTTTGCATCTTTTCGCAG

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|125097850|gb|EL154176.1|EL154176
EST:     CTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGC                         CATTGAGGCAGCTTGTGCTGCGCATCCAACAGCGGATGTATTCATCA
genomic: CTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttg ... tgttatacagCATTGAGGCAGCTTGTGCTGCGCATCCAACAGCGGATGTATTCATCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgagaggaactaactatgtgaaaattttgttttaacttgttttctgttatacagCATTGAGGCAGCTTGTGCTGCGCATCCAACAGCGGATGTATTCATCAACTTTGCATCTTTTAGGAG
                                    cttgttttct  CT-rich tract
                     aaaattttgttttaac  TA-rich tract