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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattgtctgaagttttgaagctaaaatcagattaaatataaaatatctgaacattgcctcccaaggaatctaatcccatcttgatgtgcttttgcttagGATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAGGATCAGAGACTTCCTCACCACAAGGATCCTAAAGAGTTTGTATCGTTGG

Basic information

species Arabidopsis thaliana
transcript AT4G14716.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14716.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g06620.1 (Oryza sativa), 3'ss of exon 1
gaattgtctgaagttttgaagctaaaatcagattaaatataaaatatctgaacattgcc-tcccaaggaatctaatcccatcttgatgtgcttttgcttagGATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAGGATCAGAGACTTCCTCACCACAAGGATCCTAAAGAGTTTGTATCGTTGG
||     |  || || ||     |   | | | || |  | | |||   |   ||  |  |  | |    |        || |||        |   ||||||||| |  || || || ||  |||||||||| |||||||| ||||||||||| ||||| |||||||| ||    || || ||||| ||  |  |  |  
gatacaacgtaaattatgttag-atgtttaaactagacctcagatagtgggttatacctgtttctacttgttctgaagtatgttgtccattgctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTA

upper sequence: AT4G14716.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g28350.1 (Oryza sativa), 3'ss of exon 1
gaattgtctgaagttttgaagctaaaatcagattaaatataaaatatctgaacattgcc--tcccaaggaatctaatcccatcttgatgtgcttttgctta---gGATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAGGATCAGAGACTTCCTCACCACAAGGATCCTAAAGAGTTTGTAT-CGTTGG
          |  | ||| |  || | |||  |    | |    | | | |    ||    ||     || | |  | |  |  |  |   |        |   |||||| |     || |||||  |||| ||||| ||||||||||| |||||||| ||||| |||||||| |||   || || ||||| ||  |    |||| 
----cagacaatttattgtaagtaca-tcatttgtggtgtgcggtgtttaagttctggtaatcttgttgattgttgtactgttctttttccccccaaaaaaaaagGATGGTAAGACGGAGGTGATAGAAGCATGGTACATGGATGATAGCGAAGAGGACCAGAGGCTTCCTCATCACCGCGAACCCAAAGAATTCATTCATGTTG-

upper sequence: AT4G14716.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G38940.3 (Glycine max), 3'ss of exon 1
gaattgtctgaagttttgaagctaaaatcagattaaatataaaatatctgaacattgcctcccaaggaatctaatcccatcttgatgt-gcttttgcttagGATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAGGATCAGAGACTTCCTCACCACAAGGATCCTAAAGAGTTTGTATCGTTGG
   || || |  |||| || | || |   |   |  ||  | ||   |  |  | |           | | |  |   |     | ||   |||| | ||||||    |||| |||||  ||||||| ||||| |||||||||||||| || ||||| ||||| || |||||||| || || || |||||||| |||||||
-ctttttcagttgtttagaggttatatgaattcttcattaagaaatcccaagaaataagaggatcttattttttttttaatcaaacgtcattttttcatagGATCCACGAGAGGAAGTCCTTCAAGCATGGTACATGGATGATAGTGATGAAGATCAAAGACTCCCCCACCACAAAGAACCCAAGGAGTTTGTCTCGTTGG

upper sequence: AT4G14716.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G28860.2 (Glycine max), 3'ss of exon 1
gaattgtctgaagttttgaagctaaaatcagattaaatataaaatatctgaacattgcctcccaaggaatctaatcccatcttgatgtgcttttgcttagGATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAGGATCAGAGACTTCCTCACCACAAGGATCCTAAAGAGTTTGTATCGTTGG
    ||     | ||||  || |      || ||| ||  |   |   | || |   ||    ||  ||    |||  ||  |  |    |||| | ||||||    |||| || ||  ||||||| ||||| |||||||||||||| || ||||| ||||| || |||||||| || || || |||||||| |||||||
ctgctgctgctactttttcagttgttgagaggttatatgaattcttcattaagaactcccgataaataagaggatcttattatttttcattttttcatagGATCCACGAGAGGATGTCCTTCAAGCCTGGTACATGGATGATAGTGATGAAGATCAAAGACTCCCCCACCACAAAGAACCCAAGGAGTTTGTCTCGTTGG

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|19878312|gb|AU239143.1|AU239143
EST:     AAGAAGGACGTAAGACATCACNGAGGAACACGATGGGTGAAGCGGTCAAG                         GATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAG
genomic: AAGAAGGAC-TAAGACATCAC-GAGGAACACGATGGGTGAAGCGGTCAAGgtatgttttt ... ttttgcttagGATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAG
EST: gi|124852479|gb|EH936916.1|EH936916
EST:     CGAAGAAGGACTAAGACATCACGAGGAACACGATGGGTGAAGCGGTCAAG                         GATGGGAGAGAAGAAGTGATTCAAGCTTGG
genomic: CGAAGAAGGACTAAGACATCACGAGGAACACGATGGGTGAAGCGGTCAAGgtatgttttt ... ttttgcttagGATGGGAGAGAAGAAGTGATTCAAGCTTGG
EST: gi|19874934|gb|AU235765.1|AU235765
EST:     CGAAGAAGGACTAAGACATCACGAGGAACACGATGGGTGAAGCGGTCAAG                         GATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAG
genomic: CGAAGAAGGACTAAGACATCACGAGGAACACGATGGGTGAAGCGGTCAAGgtatgttttt ... ttttgcttagGATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAG
EST: gi|124723740|gb|EH815142.1|EH815142
EST:     CGAAGAAGGACTAAGACATCACGAGGAACACGATGGGTGAAGCGGTCAAG                         GATGGGAGAGAAGAAGTGA
genomic: CGAAGAAGGACTAAGACATCACGAGGAACACGATGGGTGAAGCGGTCAAGgtatgttttt ... ttttgcttagGATGGGAGAGAAGAAGTGA
EST: gi|124741751|gb|EH832913.1|EH832913
EST:     CGAAGAAGGACTAAGACATCACGAGGAACACGATGGGTGAAGCGGTCAAG                         GATGGGAGAGAAGAAGTG
genomic: CGAAGAAGGACTAAGACATCACGAGGAACACGATGGGTGAAGCGGTCAAGgtatgttttt ... ttttgcttagGATGGGAGAGAAGAAGTG
EST: gi|152035832|gb|BP862940.2|BP862940
EST:     AAGAAGGACTAAGACATCACGAGGAACAGGATGGGTGAAGGGGTCAAG                         GATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAG
genomic: AAGAAGGACTAAGACATCACGAGGAACACGATGGGTGAAGCGGTCAAGgtatgttttt ... ttttgcttagGATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAG
EST: gi|124985775|gb|EL058343.1|EL058343
EST:     CGAAGAAGGACTAAGACATCACGAGGAACACGATGGGTGAAGCGGTCAAG                         GATGGGAGAGAAGAA
genomic: CGAAGAAGGACTAAGACATCACGAGGAACACGATGGGTGAAGCGGTCAAGgtatgttttt ... ttttgcttagGATGGGAGAGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgaacattgcctcccaaggaatctaatcccatcttgatgtgcttttgcttagGATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAGGATCAGAGACTTCCTCACCACAAGGATCCTAAAGAGTTTGTATCGTTGG
                                            cttttgctt  CT-rich tract
                      aatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattgtctgaagttttgaagctaaaatcagattaaatataaaatatctgaacattgcctcccaaggaatctaatcccatcttgatgtgcttttgcttagGATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAGGATCAGAGACTTCCTCACCACAAGGATCCTAAAGAGTTTGTATCGTTGG

- - - - - - gttttga
- - - - - - - - - - - -aaaatca
- - - - - - - - - - - - - - - - - - - ataaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatccca