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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC

Basic information

species Arabidopsis thaliana
transcript AT5G45620.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 1
---ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
   ||   | ||   ||||  |  |   ||  | |||   |     | ||||| ||  |||     | ||  ||| | | |     ||   || ||  | ||| | |||||  |  | || ||| ||||  |||||||||||||||| || |||||||||||||||||||| || ||||||||||| || ||  | |  || |
aaatttactcttgttgtttgaaccttgcttaggtttgtaactgctgtgttgtgcct--tctgcgtttttgcaattctaacagcggcatccattctc-ctacagACGGGTGACACCCTCATACAGCTCTACAACAATTTCATCACTGATTTCGAGACGAAGATCAATCTTCTCAAACTTGCGCATTTCGCGGTCATCGCTTCGC

upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
ttaggttttagggtttatagatcaattttg-attgcttc--caagtttttgtgtctgatcttaacctgtgt-cattgttataatataattttttttcattt-----cagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
           | |  ||   ||||| ||| ||| ||||  |||   | ||  |  | | |||||   ||  || |  |  |||   |      ||||||      ||| |||| ||  |  | || ||| ||||  ||||||||||| ||||||| |||||||||||||||||||| || ||||| || || || ||  | |  || |
---------tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcattcattctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC

upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G083076_T03 (Zea mays), 3'ss of exon 2
ttaggttttagggtttatagatcaattttgattgcttc-caagtttttgtgtctg-atcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
 ||   |||     || || ||   |     |   ||| |  | |  | | |||| |   |    | | | ||  || |||||| |  |||| |   | ||| | || ||  || | |||||| ||||  |||||||||||||||| |||||||| ||||| ||||| || |||||||| |||||||| ||| | |  ||||
-taaagtttgccaattttatattgttccaagtcatttcacctgctgctatttctgtactcttttgtcttttatgattctaatatcaccttttctt-ctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATCACTGATTTTGAGACCAAGATTAATCTGCTCAAGCTTGCCCATTTTGCGGTGATAGCTTCTC

upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G34310.1 (Glycine max), 3'ss of exon 1
-ttaggtttta--gggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcattt-cagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
 ||   || ||  |     |||     | | ||||    | ||  || || | | |  | | ||  | | |  |||  | |   |  ||  | |  |||| ||||||||||||||||| || || || ||||||||||||||||| |||||||||||||| ||||| ||||| |||||||| |||||||||||  | || ||||
gttgacttctattgaaacaatattcatactctgatg---tgcatattcttat-tatagtttaaatttatttgtttgacaaacggttcttcctataaattttcagGCTGGTGATGCTTTAATACAATTATATCACAATTTCATCACAGACTTTGAGACGAAAATCAACCTTCTCAAGCTTGCACATTTTGCTGTTATAGTTTCTC

upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G34310.2 (Glycine max), 3'ss of exon 2
-ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTT-CTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
 | | | ||||     || |  |  ||    ||| | ||  ||  |||| | |  |  | ||||| | |||   ||  |   |    | || |  ||||     ||   |  | |||   ||   ||        || |||   ||    | | |    |  ||  |   ||  || | |      ||   |  |  |    
gtgatgctttaa----tacaattatatcacaatttcatcacagactttgagacgaaaatcaacct-tctcaagcttgcacattttgctgttatagTTTC---TCGGCAGTATTCTGAAAAAGAAGCTGCTGTTGGTT-ATCTTGGAG---GGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT

upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 1
ttaggtttta--gggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttca---tttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
 |   |||||  |     |||  |  | | ||||    | || || ||  | |   |  ||||  ||| ||  | | | ||     | ||  |  |   |||||||| |||||||| || || || || ||||||||||||||||| ||||||||||| || ||||| ||||| |||||||||||||| |||||  | || ||||
-tgacttttattgaaacaatatttgtactctgata---tgcatgtgttcttattatagtttaaa-tgtatctgtttcacaaatggttcttcctataaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAGACCAAAATCAACCTTCTCAAGCTTGCGCATTTCGCTGTTATAGTTTCTC

upper sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcattt-cagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
 | | || |      | | |||    |   |||   |    ||   ||  | |  | || |    | ||       || | |  | | ||||||||| ||||| ||||||||| | |||||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||||||  | || ||| 
-ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA

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|152034147|gb|BP868636.2|BP868636
EST:     ATCAACTCACCCTTAAGCTCGAAAAGTTCATCGCTCTCGCTGTCTTTCAG                         GCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAG
genomic: ATCAACTCACCCTTAAGCTCGAACAGTTCATCGCTCTCGCTGTCTTTCAGgtacttttgc ... ttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAG
EST: gi|116482621|gb|EG525213.1|EG525213
EST:     ATCAACTCACCCTTAAGCTCGAACAGTTCATCGCTCTCGCTGTCTTTCAG                         GCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAG
genomic: ATCAACTCACCCTTAAGCTCGAACAGTTCATCGCTCTCGCTGTCTTTCAGgtacttttgc ... ttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtctgatcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
          tcttaac  putative branch site (score: 2)
                                       ttttttttcatttc  putative PPT
                  tgtgtcattgttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG