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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgacaccaaagtctcttacttatcttgtacattactacattctgtttatcttatattgacttaaagcctattggataatcagGGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGATATGCTTCCACTGAAGGCAGGCATTGTAAGCCCTTCAATCCTTTGCTTG

Basic information

species Arabidopsis thaliana
transcript AT4G22540.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G22540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g40590.1 (Oryza sativa), 3'ss of exon 4
----gtaagtgacaccaaagtctcttact-tatcttgt--acattactacattctgtttatcttatattg--acttaaagccta--ttggata---atcagGGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGATATGCTTCCACTGAAGGCAGGCATTGTAAGCCCTTCAATCCTTTGCTTG
    | || ||       ||| | ||  |  |  |  |  || | | |  ||||   |  | ||   |||  ||| | | | ||  ||| |||   ||||||| || || ||  | |||    |  |||||||||| ||||| |||||||||||||||||||| ||     | |  || || || |||||||| ||| | |
ccacgaaattgctgtatcagtattttggtgcagttaattaacctcaatttattcaact-gtgttgagttgatactcatatcttaatttgcatatacatcagGGAAACGGGCTGATGAGAATTCTTTATGTTGCTGCATTTGCTGTCTCTGGATATGCTTCCACGGATTCTCGCCCCTGCAAACCTTTCAATCCATTGTTGG

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 4
-------gtaagtga-caccaaagtctcttacttatcttgtacattactacattctg--tttatcttatattgacttaaagcct---attggataatcagGGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGATATGCTTCCACTGAAGGCAGGCATTGTAAGCCCTTCAATCCTTTGCTTG
         |||| | |||  |  ||||  ||| ||  |||   ||| |    | |   || || | | | |  | |||    |    ||    | |||||||||||||||  | |||    |  |||||||||| |||||||||||||||||||| ||||| ||   | ||| ||| || || |||||||| |||||||
ctaccgaccaagttatcactcagttctcagactaatggtgtttcttatttatctataaattgatttaacaataccataataattttgcttctgcattcagGGGAATGGTCTGATGAGAATTCTTTATGTTGCTGCATTTGCGGTCTCTGGATATGCATCCACAGATTCCCGGCCTTGCAAACCTTTCAATCCATTGCTTG

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G409265_T01 (Zea mays), 3'ss of exon 4
-------gtaagtga-caccaaagtctcttacttatcttgtacattactacattctg--tttatctta---tattgacttaaagcctattggataatcagGGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGATATGCTTCCACTGAAGGCAGGCATTGTAAGCCCTTCAATCCTTTGCTTG
         |||| | |||  |  ||||  ||| ||  |||   ||| |    |||   || || | |   ||||    |||      |     | |||||||||||||||  | |||    |  |||| ||||| |||||||||||||||||||| ||||| ||   | | |  || || || || ||||| |||||||
ctaccaaccaagttatcactcagttctcagactaattgtgtttcttatttatctctaaattgatttgacagtattataataattttgctcctgcattcagGGGAATGGTCTGATGAGAATTATTTATGTCGCTGCATTTGCGGTCTCTGGATATGCGTCCACAGATTCCCGCCCCTGCAAACCATTTAATCCATTGCTTG

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 5
------------gtaagtgac-accaaagtctcttacttatcttgtacattactacattctgtttatcttatattgacttaaagcctattggataatcagGGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGATATGCTTCCACTGAAGGCAGGCATTGTAAGCCCTTCAATCCTTTGCTTG
             |  ||||     |||| |  |||||  | |   |  ||  |  | ||||    | ||   |           |  ||   |    |||| ||  ||||| ||||||   || ||||||| ||||||||||| ||||||||||| ||| |||||||  ||||||| || |||||||| || ||||| |
aatgctaaaatattttgtgattgttaaagacgtttactgctttaacatcttcatgaaatctgacatttttccctcattgggctttcctttttgtttctagGGAAACAGTCTCCTAAGAGTTCTACATGTTGCAGCTTTTGCGGTTTCTGGATATGCGTCCTCTGAAGGTCGGCATTGCAAACCCTTCAACCCATTGCTAG

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 3
------------gtaagtgac-accaaagtctcttacttatcttgtacattactacattctgtttatcttatattgacttaaagcctattggataatcagGGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGATATGCTTCCACTGAAGGCAGGCATTGTAAGCCCTTCAATCCTTTGCTTG
             |  ||||     |||| |  |||||  | |   |  ||  |  | ||||    | ||   |           |  ||   |    |||| ||  ||||| ||||||   || ||||||| ||||||||||| ||||||||||| ||| |||||||  ||||||| || |||||||| || ||| | |
aatgctaaaatattttgtgattgttaaagacgtttactgctttaacatcttcatgaaatctgacatttttccctcattgggctttcctttttgtttctagGGAAACAGTCTCCTAAGAGTTCTACATGTTGCAGCTTTTGCGGTTTCTGGATATGCGTCCTCTGAAGGTCGGCATTGCAAACCCTTCAACCCATTGTTAG

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|164141356|gb|ES079431.1|ES079431
EST:     GTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCT                         GGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGA
genomic: GTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCTgtaagtgaca ... ggataatcagGGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacattactacattctgtttatcttatattgacttaaagcctattggataatcagGGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGATATGCTTCCACTGAAGGCAGGCATTGTAAGCCCTTCAATCCTTTGCTTG
                          tattgac  putative branch site (score: 2)
                 tttatcttatattgac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgacaccaaagtctcttacttatcttgtacattactacattctgtttatcttatattgacttaaagcctattggataatcagGGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGATATGCTTCCACTGAAGGCAGGCATTGTAAGCCCTTCAATCCTTTGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG