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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagagttttattcaaccaatttcattgttcaatacttagcatttactatgatttgtgttatgaaaccattcgatttttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAA

Basic information

species Arabidopsis thaliana
transcript AT1G17880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
-----gtatagagttttattcaaccaatttcattgttcaatacttagcatt-tactatgatttgtg---ttatgaaaccattcgatttttactt---gcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAA
      ||  | | ||   |      ||   ||  || || ||   | ||| | || ||   | ||   | ||   |  | | | | |  | ||   |||| ||||||||||| || |||||||| |  || ||||||||||||||||||||||||||  | || ||| | ||||| |||  |||||| | ||| ||||| 
aagatatactgggcttgtattttgggatccgatcttttaa-acaatgtattgtgctgtggcctttggattcatattaatacttgttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG

upper sequence: AT1G17880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G131577_T03 (Zea mays), 3'ss of exon 2
---gtatagagttttattcaaccaatttcat-tgttcaatact----tagcatttactatgatttgtgttatgaa--accattcgattt--ttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAA
    |||| | | |  | | |    | |||| ||| |  |||     ||| |  | ||    | |   |||| |   |  | | | |||  ||  | |||| ||||||||||| || |||||||| |  || || ||||| || |||||||| ||||| || || ||||| ||||| ||| ||||||| | ||||||||| 
gttatatata-tatggtaccattgctgtcatatgtacggtaccggtctaggaagtcctggattcttacttataagttataactagctttggttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACGACCACAGATGATAAAAGGCTTCAGAGCACCCTGAAAAGAATAGGAGTGAACACCATTCCTGGTATTGAAGAG

upper sequence: AT1G17880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G110116_T01 (Zea mays), 3'ss of exon 2
---gtatagagttttattcaaccaatttcattgttca-atacttagcattta---ctatgattt-gtgtta-tgaaaccattcgattt---ttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAA
   | |   |    | ||       |     |||||| | | | | | | |    | ||  |    || ||   ||   ||  |        | || |||| ||||||||||| || ||||||||||  || || ||||||||| ||||||| |||||  | || || || || |  ||| ||||||| | ||| || || 
caagcacctaagcctgttgggtttgtgat-ctgttcatagagtcaacttctggacccatagtcccatgctaactaatttatgagggacaaaatgctggcagGAAGAAGAAGGCAGTTCACAAGACCACGACCACCGATGACAAGCGGCTTCAGAGCACCTTGAAAAGGATCGGGGGGAACACCATTCCTGGTATCGAGGAG

upper sequence: AT1G17880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0053g00620.t01 (Vitis vinifera), 3'ss of exon 2
---gtatagagttt-tattcaaccaatttcattgttcaatacttag---catttactatgatttgtgttatgaaaccat-tcgatttttact----tgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAA
   || |    ||  | || |     | | ||| |  |  |||| |   |   | ||||  || ||  |||  |    | || | ||||  |    |||||||||||||||||||| ||||| || |  |||||||||||||| |||||||||||||| || |||||||| ||||| ||  |||| || |||||||| || 
tgggtttgatattggtgttgatgtggtgtgatt-tatacaacttggattcccctgctatacttggttatatttattattatcaactttttttgtgctgcagAAAGAAGAAGGCTGTTCACAAAACAACCACAACTGATGACAAAAGGCTTCAAAGCACCCTAAAGAGAATAGGAGTCAATGCCATACCTGCTATTGAGGAG

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|164188250|gb|EL977905.1|EL977905
EST:     TGGCGGAAAGGGTACAGTCAGAAG                         AAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTCCA
genomic: TGGCGGAAAGGGTACTGTCAGAAGgtatagagtt ... ttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCA
EST: gi|125209612|gb|EL224566.1|EL224566
EST:     TGGCGGAAAGGGTACTGTCAGAAG                         AAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCA
genomic: TGGCGGAAAGGGTACTGTCAGAAGgtatagagtt ... ttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCA
EST: gi|125216393|gb|EL230476.1|EL230476
EST:     AGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAG                         AAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCA
genomic: AGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAGgtatagagtt ... ttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCA
EST: gi|125016033|gb|EL088302.1|EL088302
EST:     ATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAG                         AAAGAAGAAGGCTGTGCACAAGACCAATACAACT
genomic: ATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAGgtatagagtt ... ttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACT
EST: gi|152035741|gb|BP855298.2|BP855298
EST:     ATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAG                         AAAGAAGAAGGCTGTGCACAAGACCAATACAAGCTGATGACAAGAGGCTTC
genomic: ATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAGgtatagagtt ... ttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAA-CTGATGACAAGAGGCTTC
EST: gi|47829080|gb|CK118764.1|CK118764
EST:     ATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAG                         AAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCA
genomic: ATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAGgtatagagtt ... ttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCA
EST: gi|125131235|gb|EL173979.1|EL173979
EST:     ATGAAGATGGCTAATACC-TCCGCACTGGCGGAAAGGGTACTGTCAGAAG                         AAAGAAGAAGGCTGTGCACAAGACCAAT
genomic: ATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAGgtatagagtt ... ttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAAT
EST: gi|86074372|gb|DR370129.1|DR370129
EST:     ATGAAGATGGCTAACACCGTCCGCACTGGCGGAAAGGGTACAGTCAGAAG                         AAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTCCA
genomic: ATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAGgtatagagtt ... ttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacttagcatttactatgatttgtgttatgaaaccattcgatttttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAA
                                          tttttactt  CT-rich tract
         atttactatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagagttttattcaaccaatttcattgttcaatacttagcatttactatgatttgtgttatgaaaccattcgatttttacttgcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA