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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttgttttttcttttcaagttgagatatctataattctgtaacttggtgacggcattacattaacaagtgtgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G06360.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 4
----gtttgtttgttttttcttttcaagttg--agatatctataattc---tgtaacttg-gtgacggcattacatt------aacaagtgtgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG
    ||     | ||||   ||   ||  ||  |  | ||||||||     ||| |       | |  | || || |      | ||    | || | |      |||||||| |||||||| ||||| ||||||||||  || || ||||||||||||||||| ||| | ||||||
gtaagtactcatattttgggttgctaaaatgctatctttctataatctagatgtgatacacaagtcaacttttcactgttttgatcattcatatgctgtgaaacatagGTTCTCAGCAACACAATTAAGCAAAAGAGGATGGAAAAGGCTGGCAAATGGGAGGTTCCTTTGCCAAAG

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G009876_T01 (Zea mays), 3'ss of exon 4
gtttgtttgttttttcttttcaagttgagatatctataattctgtaacttggtgacggcattacattaacaagtgtgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG
||   ||  | || |    |    |  || ||  ||| || | ||||| |  | | ||||||  || |   |   | | |  |   ||||||||||| |||||||| || || ||||||||||| || || |||||||||||||| || ||||| ||||||
gtgaattactgttcttggcttctctccagctaattatgatacagtaacgtttt-atggcattg-atcactga---tatctggtgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 4
gtttgtttgttttttcttttcaagttgagatatctataattc------tgtaacttggtgacgg--cattacattaacaagtg-tgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG
 |    |    ||||   |  |||       || |  ||         | | |    || |||    ||  |||| |  | || | | |  |   | |||||| || |||||||| || || ||||||||||| || || |||||||||||||| || || || ||||||
-tacagtaacgttttaagtcaaagcaacataatttggaacagagggggtatgatacagtaacgttttatggcattgatcactgatttctggtgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 4
gtttgtttgttttttcttttcaagttgagatatctataattctgtaacttggtga--cggcattacattaacaagtgtgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG
    |  ||||  |   ||  |||  |   |  |  |  || |  |   | || |   |  |  |   | |||| | | | |||||      |||||||||||||||||||||| ||||||||||| ||||| || || |||||||| || ||||| || |||
----gcatgttcatgtcttgaaagaaggttttgcctttttttttcagtcttgtaagttgaaagcaatctgacaaatttctattttt------agGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 4
gtttgtttgttttttcttttcaagttgagatatctataattctgtaacttggtgacggcattacattaacaagtgtgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG
    |  ||||  |   ||  ||| || | | | | |   | || |   | || |      ||   | |    | | | |||||      |||||||||||||||||||||| ||||||||||| ||||| || || |||||||| || ||||| || |||
----gcatgttcatgtcttgaaagatg-gttgtgtgtgtgtttgcagacttgtaag-----taatctgatggttttctattttt------agGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 4
gtttgtttgttttttcttttcaagttgag-atatctataattctgtaacttggtgacggcattacattaacaagtgtgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG
    |  ||||  |   ||  ||| ||    | | | |  || || |   | || |      ||   | |    | | |  ||||      |||||||||||||||| ||||| ||||||||||| ||||| || || |||||||| || ||||| || |||
----gcatgttcatgtcttgaaagatggttgtgtgtgtgtttttgcagacttgtaag-----taatctgatggctttctactttt------agGTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtttgttttttcttttcaagttgagatatctataattctgtaacttggtgacggcattacattaacaagtgtgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG
|| | || | | ||  | | |   ||     ||  | | |  ||||  ||       ||  |   |  |   |    |  || ||  | |||||||||||||| || || || ||||| ||||||||||||||||| |||||||| |||||||| || || 
gtctatt-gctgttgatgtacttattatcgaatacaaactcatgtacattac---atgctctttgtggatctg-acattattctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAA

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|86050590|gb|DR346345.1|DR346345
EST:     GAGCTGTTCCHGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAG                         GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
genomic: GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAGgtttgtttgt ... ttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
EST: gi|86050587|gb|DR346342.1|DR346342
EST:     GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAG                         GWTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
genomic: GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAGgtttgtttgt ... ttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
EST: gi|164175091|gb|ES188430.1|ES188430
EST:     GACACCACTCGTGCCAAG                         GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
genomic: GACACCACTCGTGCCAAGgtttgtttgt ... ttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
EST: gi|86050592|gb|DR346347.1|DR346347
EST:     GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAG                         GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAA
genomic: GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAGgtttgtttgt ... ttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAA
EST: gi|86050595|gb|DR346350.1|DR346350
EST:     GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAG                         GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
genomic: GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAGgtttgtttgt ... ttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
EST: gi|86050588|gb|DR346343.1|DR346343
EST:     GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAG                         GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
genomic: GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAGgtttgtttgt ... ttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
EST: gi|116396688|gb|EG439280.1|EG439280
EST:     GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAG                         GTTCTTAGCAACACCATT
genomic: GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAGgtttgtttgt ... ttgggtgtagGTTCTTAGCAACACCATT
EST: gi|86050586|gb|DR346341.1|DR346341
EST:     GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAG                         GTTCTTAGCAACACCATTAAACA
genomic: GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAGgtttgtttgt ... ttgggtgtagGTTCTTAGCAACACCATTAAACA
EST: gi|86050593|gb|DR346348.1|DR346348
EST:     GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAG                         GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
genomic: GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAGgtttgtttgt ... ttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
EST: gi|125282409|gb|EL296494.1|EL296494
EST:     CTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAG                         GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
genomic: CTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAGgtttgtttgt ... ttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
EST: gi|86072911|gb|DR368668.1|DR368668
EST:     GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAG                         GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG
genomic: GAGCTGTTCCTGCTTATCTTCTTGATCGTGAAGACACCACTCGTGCCAAGgtttgtttgt ... ttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattctgtaacttggtgacggcattacattaacaagtgtgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG
                          cattaac  putative branch site (score: 2)
                                        tgttttt  putative PPT
                      attacattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttgttttttcttttcaagttgagatatctataattctgtaacttggtgacggcattacattaacaagtgtgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG