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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGATCTCGGAAAGTAAATCGCAGCCATGGCGGAAAAAGCTGTCACTATCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttcccatctctatgttccattttgcaatctcacagtgttacgtcttcgctgtatcgaatgataaaaactatagtttaggtagaaacaatcttata...

Basic information

species Arabidopsis thaliana
transcript AT5G28060.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA20G37190.1 (Glycine max), 5'ss of exon 1
GACTGATCTCGGAAA-GTAAATCGCAGCCATGGCGGAAAAAGCTGTCACTATCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttcccat---------ctctatgttccattttgcaatctcacagtgttacgtcttcgctgtatcgaatgataaaaactatagtttaggtagaaacaatcttata
   || ||    |   |    ||     ||||||||| || || ||||| ||| | |||||||| |||||||| |||||||||||| |||||||||||||||| ||||    |         |  |||||| |   ||   || | | |  ||| | |||     || |||| |   ||||| | |   | |      | | |       
-GTTGCTCCTATAGCCGGCGCTCAACAACATGGCGGACAAGGCAGTCACCATCCGAACCAGAAAGTTCATGACAAACAGGCTTCTCTCCAGAAAGCAATTCgtaagtttttcttgttcttcgcattatgttacgcattttgattttatatagttccctct--atcgtttcgattctgaaaaaatgttactcattcgagaccca-------

upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA10G30200.1 (Glycine max), 5'ss of exon 1
GACTGATCTCGGAAAGTAAATCGCA-GCCATGGCGGAAAAAGCTGTCACTATCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttcccatctctatgttccattttgcaatctcacagtgttacgtcttcgctgtatcgaatgataaaaactatagtttagg---tagaaacaatcttata
   || ||  | |      |    |   ||||||||| || || ||||| ||| | ||||| || || ||||| |||||||||||| |||||||||| |||||  |||    ||  |  || |  |  |     ||     |  | | | ||   | | | || |        |||| |||| |    |  || |||| | |  
-GTTGCTCCAGTAGCCGGCACTAAACAACATGGCGGACAAGGCAGTCACCATCCGAACCAGGAAGTTTATGACAAACAGGCTTCTCTCCAGAAAGCAGTTCgtacgtttttctcgtttcgtcctctgatcttcgctttatatcatgcattttgattttgtagagttccct---ctatcgtttcgattctgaaagcaatgtcact

upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA19G43190.1 (Glycine max), 5'ss of exon 1
GACTGATCTCGGAAAGTAAATCGCAGCCATGGCGGAAAAAGCTGTCACTATCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttcccatctctatgttccattttgcaatctcacagtgt-tacgtcttcgctgtatcgaatgataaaaactata-gtttaggtagaaacaatcttata
| |  | |||    | | ||  | |   |||||||| || ||||| || ||| | ||| |||| ||||||||||||||||||||  |||| ||||| || ||||||| || | ||  |      ||| || |     | |    ||  |  |||   ||||   |    |   ||||  | |||  |  || |  | ||   
GGCACACCTCACTCACTGAACGGTAAGTATGGCGGACAAGGCTGTTACAATCCGAACCCGAAAGTTCATGACCAACAGGCTTCTTTCCAGGAAGCAGTTTgtgagtttccctttcccttccttttttcgctacaaatctgcacataattactcgaaatatcactttcggagtcctatttgattactttcaagctttgttt--

upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA03G40530.1 (Glycine max), 5'ss of exon 1
GACTGATCTCGGAAAGTAAATCGCAGCCATGGCGGAAAAAGCTGTCACTATCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttcccatctctatgttccattttgcaatctcacagtgtta-----cgtcttcgctgtatcgaatgataaaaactatagtttaggtagaaacaatcttata
 || | || |  | | | ||  | |   |||||||| || ||||| || ||| | ||| |||| ||||||||||||||||||||  |||| ||||| || ||||||| || | | |    | ||  |  | | || | |   | |     |   ||| | ||      |||| |    | |  |||   |   ||    |     
TACAGCTCACACACACTGAACGGTAAGTATGGCGGACAAGGCTGTTACAATCCGAACCCGAAAGTTCATGACCAACAGGCTTCTTTCCAGGAAGCAGTTTgtgagtttcccttttttctctacaaatctccacctaataacttgaaatatcactttcccagtcatatttgattatttttctgctttgttttttaattcgc-----

upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv14s0030g01620.t01 (Vitis vinifera), 5'ss of exon 1
GACTGATCTCGGAAAGTAAATCGCAGCCATGGCGGAAAAAGCTGTCACTATCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttcccatctctatgttccattttgcaatctcacagtgttacgtcttcgctgtatcgaatgataaaaactatagtttaggtagaaacaatcttata-----
    ||   | ||    ||    || | |||||||| || || || || ||| | |||||||| ||||||||||||||||||||  |  | ||||| || ||||||| || | |||   | |  ||| |     |   |     | |     |  | |   |||  |     || || ||    ||||  |||| |  |      
CCTCGACAGCCGACTCCAAGCAACAACAATGGCGGACAAGGCCGTTACCATCCGAACCAGAAAGTTCATGACCAACAGGCTTCTTTCTCGCAAGCAGTTTgtgagtttccttttct---tcctgtttggttccttggaaagcaaaagaaaatgaagga--aaatttttgttcctgtatttatcttagattcaatttactttgttc

upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 1
GACTGATCTCGGAAAGTAAATCGCAGC--CATGGCGGAAAAAGCTGTCACTATCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttcccatctctatgttccattttgcaatctcacagtgttacgtcttcgctgtatcgaatgataaaaactatagtttag--gtagaaacaatcttata
  |||| | |        |   |||||  |||||| || || ||   |||| |  | ||  | || ||||||||||||||||| |||||||| ||||| ||||| ||  ||| |  |    || |    |      |    |      | |||   |||| |   | || | |  | | | || |  || |     |  |   |
--CTGAGCCCCAGCCAGCAGCAGCAGCATCATGGCTGACAAGGCGTGCACTGTGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcacccgtggcctcctttctcgcttagggtttctggaacattggctt--gtgtaacacctcattagagttttcgcttggttgtggttgtgacttctca

upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S37_112V6.1 (Physcomitrella patens), 5'ss of exon 1
GACTGATCTCGGAAAGTAAATCGCAGC--CATGGCGGAAAAAGCTGTCACTATCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagt--tcccatctctatgttccattttgcaatctcacagtgttacgtcttcgctgtatcgaatgataaaaactatagtttaggtagaaacaatcttata
 | ||  || || ||| |  || ||||  ||||||||| || ||   |||  |  | ||  | || |||||||||||||| || |||||||||||||| ||||| ||     |   | ||    ||| || |     |   | || |  |  || | | || | || |||      ||    || || |        |  | | 
-ATTG-CCTTGGTAAGCAGGTCCCAGCAACATGGCGGACAAGGCGTGCACCGTGCGCACTCGCAAATTCATGACCAACAGACTGCTCGCCAGAAAGCAGTTCgtaagcagcgctggccctcctctccgttctttctcccatcggtttcccaactactcggt-tggattgagcttttctgggattgagctcttgttggttctgt-

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|152034225|gb|BP822397.2|BP822397
EST:     CAGGACCAGAAACTTCATGACCAACAGGCCTTCTCGCCAGAAAGCAATTC                         GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTCTCAAAG
genomic: CAGGACCAGAAACTTCATGACCAACAGGC-TTCTCGCCAGAAAGCAATTCgtgagttccc ... attaatgtagGTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
EST: gi|164180694|gb|ES018222.1|ES018222
EST:     GACCAACAGGCTTCTCGCCAGAAAGCAATTC                         GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
genomic: GACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttccc ... attaatgtagGTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
EST: gi|152034969|gb|BP841119.2|BP841119
EST:     TCAGGAACAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTC                         GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
genomic: TCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttccc ... attaatgtagGTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
EST: gi|124724569|gb|EH815971.1|EH815971
EST:     TCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTC                         GTTATTGATGTTCTTCATCCTGGAAG
genomic: TCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttccc ... attaatgtagGTTATTGATGTTCTTCATCCTGGAAG
EST: gi|125327573|gb|EL341653.1|EL341653
EST:     CTTCTCGCCAGAAAGCAATTC                         GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
genomic: CTTCTCGCCAGAAAGCAATTCgtgagttccc ... attaatgtagGTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
EST: gi|86084565|gb|DR380324.1|DR380324
EST:     TCAGGACCAGAAACTTCATGACCAACA-GCTTCTCGCCAGAAAGCAATTC                         GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
genomic: TCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttccc ... attaatgtagGTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
EST: gi|86078425|gb|DR374182.1|DR374182
EST:     TCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTC                         GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
genomic: TCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttccc ... attaatgtagGTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
EST: gi|124943338|gb|EL019527.1|EL019527
EST:     TCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTC                         GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAGG
genomic: TCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttccc ... attaatgtagGTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAGG
EST: gi|86081226|gb|DR376983.1|DR376983
EST:     TCAGGACCAGAAACTTCATGACCWACAGGCTTCTCGCCAGAAAGCAATTC                         GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
genomic: TCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttccc ... attaatgtagGTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
EST: gi|124942113|gb|EL018409.1|EL018409
EST:     CTTCTCGCCAGAAAGCAATTC                         GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG
genomic: CTTCTCGCCAGAAAGCAATTCgtgagttccc ... attaatgtagGTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTGATCTCGGAAAGTAAATCGCAGCCATGGCGGAAAAAGCTGTCACTATCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttcccatctctatgttccattttgcaatctcacagtgttacgtcttcgctgtatcgaatgataaaaactatagtttaggtagaaacaatcttata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccatctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtagaaa