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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtactaaaaccatgttgctttaattttctgaggataatcttactttcgaatttactgattgttcttggcatttgccgtcttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G59350.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G59350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G001668_T01 (Zea mays), 3'ss of exon 6
----------gttagtacta-aaaccatgttgctttaattttctgaggataatcttactttcgaatttactgattgttcttggcatttgccgtcttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG
            |  |  || |||||       ||  ||      | | ||        ||     || |||| |  | |   ||||| |  | ||   ||||||||||||||||| ||||||||||||| |||||||||||||| ||||| |   | ||||||||||||||||| || |  || || |||
caggtgttgttcttctgttagaaaccccagaagttagatcagaaaaaggtagggaagtattta---tttctgacttctatgtacattt-ctttgtttctttcagGCTACTCCAAGGTTAAGTGAAGACAAGGTGAAGCAATGTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAG

upper sequence: AT3G59350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G071877_T01 (Zea mays), 3'ss of exon 6
--------gttagtactaaaaccatgttgctttaattttctgaggataatcttactttcgaatttactgattgttcttggcatttgccgtcttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG
         ||   |   |||||        |  ||      | | ||     |  | |   | |      | || |  |||||| |  | ||    |||||||||||||||| | ||||||||||| |||||||||||||| ||||| |   | ||||||||||||||||| || |  || || |||
gatggtattttgtcagagaaaccccagaagctagatcagaaaaaggtagggaaatatacatttctgacttgttttatctgcattt-ctttgtttctgtcagGCTACTCCAAGGTTGAGTGAAGACAAGGTGAAGCAATGTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAG

upper sequence: AT3G59350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G029530_T01 (Zea mays), 3'ss of exon 6
----------gttagtactaaaaccatgttgctttaattttctgaggataatcttactttcgaatttactgattgttcttggcatttgccgtcttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG
           | || || |||      | |||      ||  |||   |    ||||||| |  ||| ||| |    ||    | |    | || | ||||||| || || ||  | | ||| |||| ||| || |||||||||||||||| | | ||||||||||||||||| || |  ||||| |||
ctctaaacttttgagcacgaaatttgcat-gctaatgaattgggagctaagcactactttccagattaatgactaaa-ttattgtatattttattta-ttcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG

upper sequence: AT3G59350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G029530_T02 (Zea mays), 3'ss of exon 6
----------gttagtactaaaaccatgttgctttaattttctgaggataatcttactttcgaatttactgattgttcttggcatttgccgtcttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG-------------
           | || || |||      | |||      ||  |||   |    ||||||| |  ||| ||| |    ||    | |    | || | ||||||| || || ||  | | ||| |||| ||| || |||||||||||||||| | | ||||||||||||||||| || |  ||||| |||             
ctctaaacttttgagcacgaaatttgcat-gctaatgaattgggagctaagcactactttccagattaatgactaaa-ttattgtatattttattta-ttcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGGTCTGGCTTCAAT

upper sequence: AT3G59350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 7
-----------gttagtactaaaaccatgttgctttaattttctgaggata-atcttactttcgaatttactgattgttcttggcatttgccgtcttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG
           | |   ||| | |||   | |||    ||||   |  ||  | |     ||   |   |  |||  ||  | |   |||   | ||   |  |||||||||||||  |||||||||| |||||||| || || ||||| |||||||| ||||||||||| || |||||||  ||||| |||
gtcagtgtgctgcttaaactcatacctcatcgctgctgtttttcaatcatttaccactggttgtcagccatagatattttgttgatattgatatttt--ttgtagGCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG

upper sequence: AT3G59350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 7
------------------gttagtactaaaaccatgttgctttaattttctgaggataatcttactttcgaatttactgattgttcttggcatttgccgtcttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG
                    |  |||   | || || ||||    ||   | |    |  ||   | |||    ||   ||| || ||| ||||     | ||   |  |||||||||||||  |||||||||| |||||||| || || ||||| |||||||| ||||||||||| || || ||||  ||||| |||
gtcagtgtgtctgcttaaactcatacctcatccgtgctgctgcttttcaatcatttaacactggttgtcggccataggtatt-ttgttgacattgatattttt--ttgtagGCTACTCCAAGATTAAGTGAAGATAAAGTGAAACAGTGCGTTGACCCAAAACTGAAGGGAGAATACCCCCCCAAAGGAGTTGCTAAG

upper sequence: AT3G59350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gttagt--actaaaaccatgttgctttaattttctgaggataatcttactttcgaatttactgattgttcttggcatttgccgtcttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG
                                          || ||  ||  |   | | |    ||  | | ||    ||    || ||||   || ||   ||  |   |    |   |  |  | |  | ||||||||||||| || |||||||||||||| || |||||||| ||||| ||||||||||||||||||||||| ||||  ||||| |||
gtgggttttttcttctttttctgcctatttgcttaaaagccttttgttcacccagtgcctttcaagtttctctactccaaattgcttttctttgatatatatctataatc--taaagtgaacatttctcatcttagGCTACTCCAAGACTGAGTGAAGACAAAGTTAAACAATGTGTAGATCCCAAACTAAAGGGAGAATATCCTCCGAAAGGAGTTGCTAAG

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|124886822|gb|EH965724.1|EH965724
EST:     TCAACAAAGTCTTGTTACTTGG                         GCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAA
genomic: TCAACAAAGTCTTGTTACTTGGgttagtacta ... ttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAA
EST: gi|124844458|gb|EH928895.1|EH928895
EST:     AACCCGTCGATCATACGATGCCTCGTGGTCAACAAAGTCTTGTTACTTGG                         GCTACTCCAAGGCTAAG
genomic: AACCCGTCGATCATACGATGCCTCGTGGTCAACAAAGTCTTGTTACTTGGgttagtacta ... ttaacttcagGCTACTCCAAGGCTAAG
EST: gi|86079614|gb|DR375371.1|DR375371
EST:     AACCCGTCGATCATACGATGCCTCGTGGTCAACAAAGTCTTGTTACTTGG                         GCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAA
genomic: AACCCGTCGATCATACGATGCCTCGTGGTCAACAAAGTCTTGTTACTTGGgttagtacta ... ttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatcttactttcgaatttactgattgttcttggcatttgccgtcttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG
                                           tcttaac  putative branch site (score: 2)
                                        ccgtctt  CT-rich tract
              aatttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtactaaaaccatgttgctttaattttctgaggataatcttactttcgaatttactgattgttcttggcatttgccgtcttaacttcagGCTACTCCAAGGCTAAGTGAAGACAAAGTGAAGCAATGTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG