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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttaaatattctcggttcaaacttgtcttggtttactatctagaaatcttgtatataaaacgctgctttttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG

Basic information

species Arabidopsis thaliana
transcript AT1G78900.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 14
-gtatgcttaaatattct-cggttcaaacttgtcttggtttactatctagaaatcttgtatataaaacgctgctttttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG
  ||| | ||| |   ||  | |   ||      |    |  | || |   |  ||   |||  | |  |||     |  | ||||| |||||||| |||||||||||||| |||| |||||||||  | || || ||||| ||  | || ||||| ||||| || |||||||| ||||||||||
gttattcctaacttccctatgatgtcaatacaattaaaatcgccattttaca--ctaacatactatatcctg-----tactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 14
------------gtatgcttaaatattctcggttcaaacttgtcttg---gtttac---tatctagaaatcttgtatataaaacgctgctttttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG
              ||||| | |  ||     || ||  || || ||   |||  |   |   | ||  |  |||  | || ||  || ||| ||||  |||| || ||  |   |||||||| |   ||||||||||||||  | || || ||||||||  | |||||||||||||||||||| ||| | |||||||| |
tttttttcaatgaaatgctaataagtttatatttgaacattttcctgttcgttcgcatttgctttgatgttatgtg-acaatacaatgttttgtgttgcagGCGCTTGAGCCGCACTATGAGAGGGAAGATCCAGATTTCATTGATATTAGAACAAAGGCACGTGAGGTGTTGCAGAGGGAAGATGATTTAAATGAAATAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G128877_T02 (Zea mays), 3'ss of exon 14
--------gtatgcttaaatattctcggttca-----aacttgtcttggtttactatctagaaatcttgt-atataaa-acgctgctttttgtttt--agGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG
             || |||||||| | ||||        ||||| |||  ||  | || ||  ||  ||| || | |  |  |   ||| ||  ||  |||| || || || || ||||||||||| ||||||||||||||  | || |||||||| ||  | ||||||||||||||||| |||||||| ||||||||||
ttcttctttccctctcaaatattcacagttcttcatttgcttgtgttgtgttcttctccagtgatgatgttatgtgaccaaaccattttatgccttgcagGCCCTTGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 14
----------gtatgcttaaatattctcggttcaaacttgtcttggttta---ctatctagaaatcttgt-atataaa-acgctgctttttgtttt--agGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG
               || ||| || | | ||||    ||  |||| | |     | ||  |  ||  ||| || | |  |  |   ||| ||  ||  |||| || || ||||| || ||||| || ||||||||||||||  | || |||||||| ||  | ||||||||||||||||| |||||||| ||||||||||
ttgtcttatttctctctcaaacatccacagttcttcatttgcttgttgtgtccttctcccgtgatgatgttatgtgaccataccattttctgccttgcagGCCCTTGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 15
-----------------------------gtatgcttaaatattctcggttcaaacttgtcttggtttactatctagaaatctt----gtatataaaacgctgctttttgt---tttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG
                               || ||  |   ||||   ||   |    |  || |||  |  |  ||  |        | | ||| |   |  |||| ||   |||||||||| ||| | || |||||| | || ||||||||||| |||||||| |||||||||||  | || ||  |||| |||||||| || || ||||||||||
gtatgtcctaaagttggttactttgtaactcatcctccagctttctacatttgtatgcatagtgttttggttccatgactttccccgaatttttaatattttctttttggtatctttagGCACTTGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 15
-------------------------gtatgcttaaatattctcggttcaaacttgtcttggttta-----ctatctagaaatcttgtatataaaacgctgctttttgtttt--agGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG
                           ||   | || ||||  | |||    ||  ||   |||       |||  |  |     ||||   |||   |   || || |||  ||||| |||||||||| |||||| | |  ||||||||||| ||||||||||||||||||||  | |||||| |||| || ||||| || || ||||||||||
gtgtgttattaagatgttatcccttccatatattaaaattcctgattcttttttccctccattttggcctttattcaataccaccgtatcataaattttctcttgtgatttccagGCATTGGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTG

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|116463760|gb|EG506352.1|EG506352
EST:     AACATTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACG                         GCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGG
genomic: AACATTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACGgtatgcttaa ... tttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGG
EST: gi|164207249|gb|ES173179.1|ES173179
EST:     GGTTGATTTCTTACTCAAAGTATTCAACG                         GCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATT-CATCAACTATCAG
genomic: GGTTGATTTCTTACTCAAAGTATTCAACGgtatgcttaa ... tttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAAC-ATCAG
EST: gi|125205657|gb|EL220611.1|EL220611
EST:     TTGATTTCTTACTCAAAGTATTCAACG                         GCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACAT
genomic: TTGATTTCTTACTCAAAGTATTCAACGgtatgcttaa ... tttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACAT
EST: gi|124714832|gb|EH806234.1|EH806234
EST:     AACATTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACG                         GCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAAC
genomic: AACATTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACGgtatgcttaa ... tttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAAC
EST: gi|125029639|gb|EL101908.1|EL101908
EST:     AACATTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACG                         GCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACA
genomic: AACATTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACGgtatgcttaa ... tttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACA
EST: gi|116463788|gb|EG506380.1|EG506380
EST:     AACATTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACG                         GCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGG
genomic: AACATTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACGgtatgcttaa ... tttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGG
EST: gi|164221485|gb|ES026185.1|ES026185
EST:     TTTTCCCTCTGTTAATTGGTTGTATTTCTTACTCAAAGTATTCAACG                         GCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGG
genomic: TTTTCCCTCTGTTAATTGGTTG-ATTTCTTACTCAAAGTATTCAACGgtatgcttaa ... tttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGG
EST: gi|164215890|gb|ES029981.1|ES029981
EST:     TTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACG                         GCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGG
genomic: TTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACGgtatgcttaa ... tttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGG
EST: gi|164064910|gb|ES011546.1|ES011546
EST:     TTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACG                         GCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGG
genomic: TTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACGgtatgcttaa ... tttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcttggtttactatctagaaatcttgtatataaaacgctgctttttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG
                                       ctgctttttgtttt  CT-rich tract
                    aaatcttgtatataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttaaatattctcggttcaaacttgtcttggtttactatctagaaatcttgtatataaaacgctgctttttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA