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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaatggagtctcatctgaattctttgtcggtgttatttacttacaaaagcggagaagctaacatgagaatgtttatttcagTGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTCCAGAAACTGCTACTGTTGGCTCATTGAAG

Basic information

species Arabidopsis thaliana
transcript AT5G59430.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59430.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g16700.4 (Oryza sativa), 3'ss of exon 4
gtaacaatggagtctcatctgaattctttgtcggtgttatttacttacaaaagcgg--agaagctaaca-tgagaatgtttattt---cagTGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTCCAGAAACTGCTACTGTTGGCTCATTGAAG
||||   |||   |       |  | ||||    ||| |||   ||        ||  | |  |||| | ||    | ||| |     |||| |||||  |||||||||| |||| ||||||||| ||| | || ||||| ||||||||||| |||||||| ||| |||||
gtaagtttggccccatgaaaaatgtttttgatattgtaattattttggttttatggccatagtctaagactgcctgtttttctccttgcagTAAAACTTAGGATCAAGTCTTTCAAGGTGCCTGAACTTCTAATTGAGATCCCAGAAACTGCGACTGTTGGTTCACTGAAG

upper sequence: AT5G59430.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G04200.1 (Glycine max), 3'ss of exon 5
--------gtaacaatggagtctcatctgaattctttgtcggtgttatttacttacaaaagcggagaagctaacatgagaatgtttattt------cagTGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTCCAGAAACTGCTACTGTTGGCTCATTGAAG
          |   | |||||      | |  |  |  | | | | | | |  |    ||   | |   || ||||||  |||| | | |      ||||||| ||  ||||||| || ||||| |||||||||||||| || ||||||||||||||||| || || || ||  |||||
gtatgggaagattgagggagtgattctttatgtactctttgatttgactgatgtcttcaaa--ggggttcttacatgaagatgtctttcttttaaccagTGAAGCTTAGGATCAAATCATTCAGAGTGCCTGAGCTTTTTATCGAGATTCCAGAAACTGCAACCGTCGGGTCCCTGAAG

upper sequence: AT5G59430.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G14760.4 (Glycine max), 3'ss of exon 4
-----------gtaacaatggagtctcatctgaattctttgtcggtgttatttacttacaaaagcggagaagctaacatgagaatgtttattt------cagTGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTCCAGAAACTGCTACTGTTGGCTCATTGAAG
            | |    | | |    | || |||||||| |  || |   ||  | |||| |    |   || |||||  ||||| | | |      ||||||| ||  |||||||||| || || ||||| |||||||| |||||| ||||||||||||| ||  |||| || ||||||
gtatgagaagattgagggagcaattctttatgtattctttgact-tgatcgatatcttcaaagg----ggttcttacatgtaaatgtctttcttttaaccagTGAATCTTAGGATCAAGTCATTTAGAGTGCCAGAGCTTTTTATAGAGGTTCCAGAAACTGCAACAATTGGGTCCTTGAAG

upper sequence: AT5G59430.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G06680.1 (Glycine max), 3'ss of exon 4
gtaacaatggagtctcatctgaattctttgtcggtgtt---atttactta-caaaagcggagaag--ctaacatgagaatgtttattt------cagTGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTCCAGAAACTGCTACTGTTGGCTCATTGAAG
|||  |   || |        |||||||| |   |  |   ||||  | |  |    |  || ||  || |||||  ||||| | | |      ||||||| ||  |||||||||| || || ||||| |||||||| |||||| ||||||||||||| ||  |||| || ||||||
gtatgagaagattgagggagcaattctttatgtattctttgatttgatcaatatcttcaaaggagttctcacatgcaaatgtctttcttttaaccagTGAATCTTAGGATCAAGTCATTTAGAGTGCCAGAGCTTTTTATAGAGGTTCCAGAAACTGCAACAATTGGGTCCTTGAAG

upper sequence: AT5G59430.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 5
---------gtaacaatggagtctcatctgaattctttgtcggtgttatttacttacaaaagcggagaagctaacatgagaatgtttatt-------tcagTGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTCCAGAAACTGCTACTGTTGGCTCATTGAAG
               |||||||      |   | || | | |   | |||    |   | |   ||    || |  |||  |||| | |        |||||||| ||  |||||||||| ||||||||||| ||||| || |||||||||||||||||||| |||||||| ||  | |||
gtatgagagcctttgatggagtgattcttatgtactcttttgacttgattggtgtctgatattcgaagttcttatgtgaagatgtatttccttttactcagTGAAGCTTAGGATCAAGTCTTTCAGGGTGCCAGAGCTCTTTATAGAGATTCCAGAAACTGCAACTGTTGGTTCCCTCAAG

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|86037146|gb|DR332901.1|DR332901
EST:     GTAGTAGAAAAGGTCAWGGGGCATCCTTTGTGGCAAGCGACTCCCATG                         TGAAACTACGGATCA
genomic: GTAGTAGAAAAGGTCAAGGGGCATCCTTTGTGGCAAGCGACTCCCATGgtaacaatgg ... tttatttcagTGAAACTACGGATCA
EST: gi|86079249|gb|DR375006.1|DR375006
EST:     GTAGTAGAAAAGGTCAAGGGGCATCCTTTGTGGCAAGCGACTCCCATG                         TGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTC
genomic: GTAGTAGAAAAGGTCAAGGGGCATCCTTTGTGGCAAGCGACTCCCATGgtaacaatgg ... tttatttcagTGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTC
EST: gi|164128597|gb|ES039391.1|ES039391
EST:     GCGACTCCCATG                         TGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTC
genomic: GCGACTCCCATGgtaacaatgg ... tttatttcagTGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggtgttatttacttacaaaagcggagaagctaacatgagaatgtttatttcagTGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTCCAGAAACTGCTACTGTTGGCTCATTGAAG
                                             tttatttc  CT-rich tract
      ttatttacttacaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaatggagtctcatctgaattctttgtcggtgttatttacttacaaaagcggagaagctaacatgagaatgtttatttcagTGAAACTACGGATCAAGTCGTTCAGGGTGCCTGAGCTTTTCATAGAGATTCCAGAAACTGCTACTGTTGGCTCATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG