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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtctctaaccttacctaatctttgcatatgttcttgtatcctctctatatgatgctacattaaatcttgactcttatgaacaatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGAATGAGACAAAGGCAACAGTGAAGTTCCAGCTCAAGAAGGTTCTATGTAT

Basic information

species Arabidopsis thaliana
transcript AT5G22440.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g21660.1 (Oryza sativa), 3'ss of exon 4
--------gcatgtctctaaccttac--ctaatctttgcatatg-ttcttgtatcctctctatatgatgctacattaaatcttgactcttatgaacaatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGAATGAGACAAAGGCAACAGTGAAGTTCCAGCTCAAGAAGGTTCTATGTAT
        ||||   |   ||| | |      |  | |||  || ||||  |||   ||    ||| |  | |||     |||| |  ||||  ||      |||| |||||||||||||| || |  || || || ||  | || ||||| || |||||||| ||||| |||||||| |||||||| ||||||||||| || ||
tgagctatgcattgatactaccctgcggtaggtgctagcaattgattctattatttcctgcccatgtttgttcatatgcccttg-catttatcgactg----cagGCAAATTCCCAACTCTGGTGACGCATCAGGAATCACTTGAGTCCAAGGTTAATGAGACTAAGGCTACAGTGAAATTCCAGCTGAAGAAGGTTCTCTGCAT

upper sequence: AT5G22440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G023748_T02 (Zea mays), 3'ss of exon 4
gcatgtctctaaccttacctaatc---tttgcatatgttcttgtatcctctc-tatatgatgctacattaa--atcttgac---tcttatgaacaatga------acagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGAATGAGACAAAGGCAACAGTGAAGTTCCAGCTCAAGAAGGTTCTATGTAT
          |||  |||  | ||   | | ||  |   | |  | |  | | || || | | | ||||||  ||||  ||   |||| ||||   ||        ||||||||||||| ||  | || |  ||||| || ||  | || ||||| || |||||||||||||| ||||| ||||||||||| |||||||| || || ||
--------ggaacactacacactcacgtgtacaggtagacctacaactgcacatagataagg-tgcattaaggatctgcactcatcttttgaatcgtgttttactgcagGAAAATTCCCTACCTTGGTGACACACCAGGAATCCCTTGAGTCCAAGGTTAATGAGACAAAGGCTACAGTTAAGTTCCAGCTGAAGAAGGTGCTTTGCAT
















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|116413764|gb|EG456356.1|EG456356
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAAATCCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
EST: gi|86049657|gb|DR345412.1|DR345412
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTG
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTG
EST: gi|86049659|gb|DR345414.1|DR345414
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGA-TCCAAAGTG
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTG
EST: gi|125108972|gb|EL161646.1|EL161646
EST:     GTTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAAATTCCCAACTCTTGTTAGCCACCAAGAG
genomic: G-TCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAG
EST: gi|116413756|gb|EG456348.1|EG456348
EST:     TGTCATTACGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
EST: gi|86049655|gb|DR345410.1|DR345410
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAA-TTCCCAACTCTT
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTT
EST: gi|86049653|gb|DR345408.1|DR345408
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAAATTCCCAA
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAA
EST: gi|116413757|gb|EG456349.1|EG456349
EST:     TGTCATTACGCAGATTCCTCGNNNNNNNGGTCCTGGTCTCAACAAGGCAG                         GAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
EST: gi|86077020|gb|DR372777.1|DR372777
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
EST: gi|86049652|gb|DR345407.1|DR345407
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAWAATTCCCAACTCTTGTTAGCCACCA
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTTGTTAGCCACCA
EST: gi|86049658|gb|DR345413.1|DR345413
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
EST: gi|116413743|gb|EG456335.1|EG456335
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
EST: gi|86080991|gb|DR376748.1|DR376748
EST:     TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGA
EST: gi|86049656|gb|DR345411.1|DR345411
EST:     TGNCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAG                         GAAAATTTCCCAACTCTTGGTAGCCACCAAGAGTCTTT
genomic: TGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctct ... caatgaacagGAAAATT-CCCAACTCTTGTTAGCCACCAAGAGTCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcctctctatatgatgctacattaaatcttgactcttatgaacaatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGAATGAGACAAAGGCAACAGTGAAGTTCCAGCTCAAGAAGGTTCTATGTAT
                             tcttgac  putative branch site (score: 3)
                    tacattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtctctaaccttacctaatctttgcatatgttcttgtatcctctctatatgatgctacattaaatcttgactcttatgaacaatgaacagGAAAATTCCCAACTCTTGTTAGCCACCAAGAGTCTTTGGAATCCAAAGTGAATGAGACAAAGGCAACAGTGAAGTTCCAGCTCAAGAAGGTTCTATGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG