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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACAACAGCAACAAGGCGAACTTGAAGCTATATGTCAGGAGGGTGTTCATCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaaactacttgaaagacaaactaaggggttctttcaatacaaatttatgggctaaatccctaacgtgagttgcttttgcag

Basic information

species Arabidopsis thaliana
transcript AT4G24190.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 10
TTACAACAGCAACAAGGCGAACTTGAAGCTATATGTCAGGAGGGTGTTCATCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaa------actacttgaaagacaaactaaggggttctttcaatacaaatttatgggctaaatccctaacgtgagttgcttttgcag
 ||||||   |||||| | ||| | ||| | ||||| || ||||| |||||||| |||||||||||||||||||| || |||||| | || || |||||||||       |||| || |   || |   | ||  |||  |  ||  |  | |   | ||||| |  ||| |  | |  || | |   
CTACAACTCTAACAAGTCAAACCTTAAGTTGTATGTTAGAAGGGTTTTCATCTCTGATGAATTTGATGAGCTTCTTCCGAAGTATCTCAGCTTTTTGAAGgtactagattactatttcatgaacga--cacggtattccattcattgacttatgcagcctaaacctataa-gctattatctgtag---

upper sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G399073_T02 (Zea mays), 5'ss of exon 12
TTACAACAGCAACAAGGCGAACTTGAAGCTATATGTCAGGAGGGTGTTCATCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaa------actacttgaaagacaaactaaggggttctttcaatacaaatttatgggctaaatccctaacgtgagttgcttttgcag
 ||||||||||||||| | ||| | ||| | ||||| || || ||||||||||| |||||||||||||| ||||| || |||||| | || || |||| ||||        |||||| ||   ||||   |    |  ||| ||    |  |  |   |||||||  ||  ||||  | || |   ||
CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatct-tacagtgatattctctc-tag

upper sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G141931_T02 (Zea mays), 5'ss of exon 10
TTACAACAGCAACAAGGCGAACTTGAAGCTATATGTCAGGAGGGTGTTCATCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaaactacttgaaagacaaactaaggggttctttcaatacaaatttatg--------ggctaaatccctaacgtgagttgcttttgcag
 |||||||| |||||| | ||| | ||| | ||||| ||||| || |||||||| || ||||||||||| ||||| || |||||  |||| || |||||||||   || |       |||   | | |     |||||| |||  | |||        |||||||  ||| ||    |||   | || ||
CTACAACAGTAACAAGTCAAACCTCAAGTTGTATGTTAGGAGAGTTTTCATCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAGgtactgtattactgtttcaagaaacgcgtactattcaattcaatctgatgtcatagcaggctaaa--ccttacagtggttttatctgtag

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|163973367|gb|ES024615.1|ES024615
EST:     TCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAG                         GGTCTTGTTGACTCTGACACA
genomic: TCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaaactact ... gcttttgcagGGTCTTGTTGACTCTGACACA
EST: gi|164229870|gb|ES070325.1|ES070325
EST:     TCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAG                         GGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAA
genomic: TCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaaactact ... gcttttgcagGGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAA
EST: gi|125213445|gb|EL228277.1|EL228277
EST:     TCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAG                         GGTCTTGTTGACTCTGACAC
genomic: TCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaaactact ... gcttttgcagGGTCTTGTTGACTCTGACAC
EST: gi|164085056|gb|EL989225.1|EL989225
EST:     CAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAG                         GGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAA
genomic: CAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaaactact ... gcttttgcagGGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAA
EST: gi|86060423|gb|DR356180.1|DR356180
EST:     TCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAG                         GGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAATGCTT
genomic: TCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaaactact ... gcttttgcagGGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAATGCTT
EST: gi|124739022|gb|EH830184.1|EH830184
EST:     ATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAG                         GGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAAT
genomic: ATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaaactact ... gcttttgcagGGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACAACAGCAACAAGGCGAACTTGAAGCTATATGTCAGGAGGGTGTTCATCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaaactacttgaaagacaaactaaggggttctttcaatacaaatttatgggctaaatccctaacgtgagttgcttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG