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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaatttgaataaagaagcaagtccaaattcataagatcattctcaatttcattatgtagatgctaaatttagtaattctgttgttatttggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATA

Basic information

species Arabidopsis thaliana
transcript AT5G59140.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
gtaatttgaataaagaagcaagtccaaattcataagatcattctcaatttcattatgtagatgctaaatttagtaattctgttgttatttggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATA
    || |  |       ||  |    || |         | ||   |   |   |  |    ||  | |||   |     |    ||     |    ||| || ||||| ||  ||   || ||||  || |  ||||| || || |||||| | || || |||||||| |||||||||||||||||||| || || ||
---gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacac---agGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA

upper sequence: AT5G59140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g05560.t01 (Vitis vinifera), 3'ss of exon 1
gtaatttgaataaagaagcaagtccaaattcataagatcattctcaatttca---ttatgtagatgctaa-atttagtaattctgttgttatttggtatggt--agGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATA
      |  || ||        |      || |||  || ||  |||    |   || | | ||   |   | | |||  |      ||| ||||||  | |  |||  | ||  |||||  | || |||| | ||| |||||||| || ||||||||||| || || |||||||| |||||||| ||||||||||||||||||| 
------tatatgaaattttggtttatttgtcttaatttcctttgcaaccaaacggttgtttggaatttgggagtgagttctgactaggttttttggtcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATT
















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|86023419|gb|DR319172.1|DR319172
EST:     AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAG                         GTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
genomic: AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAGgtttcttctc ... ggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
EST: gi|86023423|gb|DR319176.1|DR319176
EST:     AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAG                         GTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGACATTAGCA
genomic: AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAGgtttcttctc ... ggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
EST: gi|152038451|gb|AV823441.2|AV823441
EST:     AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAG                         GTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
genomic: AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAGgtttcttctc ... ggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
EST: gi|86023421|gb|DR319174.1|DR319174
EST:     AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAG                         GTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
genomic: AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAGgtttcttctc ... ggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
EST: gi|86023424|gb|DR319177.1|DR319177
EST:     AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAG                         GTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
genomic: AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAGgtttcttctc ... ggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
EST: gi|86023422|gb|DR319175.1|DR319175
EST:     AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAG                         GTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
genomic: AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAGgtttcttctc ... ggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
EST: gi|164153591|gb|ES048256.1|ES048256
EST:     AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAG                         GTGGTTTCTCGGAATCG
genomic: AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAGgtttcttctc ... ggtatggtagGTGGTTTCTCGGAATCG
EST: gi|86077081|gb|DR372838.1|DR372838
EST:     AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAG                         GTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
genomic: AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAGgtttcttctc ... ggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
EST: gi|86023418|gb|DR319171.1|DR319171
EST:     AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAG                         GTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA
genomic: AGAAGCCGCTATGGTTTCTCAGACTATCCGAAGCATGCTCACTTCTCCAGgtttcttctc ... ggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcattatgtagatgctaaatttagtaattctgttgttatttggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATA
                tgctaaa  putative branch site (score: 2)
                   taaatttagtaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgaataaagaagcaagtccaaattcataagatcattctcaatttcattatgtagatgctaaatttagtaattctgttgttatttggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATA

- - - -gaataaa
- - - - - - - gaagcaa
- - - - - - - - - - - -ccaaatt
- - - - - - - - - - - - - - - - -aagatca