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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcttacaatctaaactagaattttgtgcattgacggtttaactccaccttctttgtttcatttaactatatgattgaccaaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCTGTTCAACATG

Basic information

species Arabidopsis thaliana
transcript AT4G25070.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G25070.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G126266_T02 (Zea mays), 3'ss of exon 9
gtttgcttacaatctaaactagaattttgtgcattgacggtttaactccaccttctttgtttcatttaactatatgattgacca--accttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCTGTTCAACATG
                        ||      |||   | || |    |  ||| |||   | || |   | |     |    |  || ||  ||||||| ||||| ||||| |||||||||||||| ||||| ||||  ||||| |||||| |||
-----------------------gttagtctgattactgcttcatactcctcttgttttagtgatatggattttaatctagttagaactttatagGAGGAGGTTGTCCTAAAAAGATGCTGGCTTGCACGCTATTGGGGCTTAGCAGTTCAATATG

upper sequence: AT4G25070.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G17390.1 (Glycine max), 3'ss of exon 9
--gtttgcttacaatctaaactagaattttgtgcattgacggtttaactccaccttctttgtttcatttaactatatgattgaccaaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCTGTTCAACATG
   | || |||| ||  ||| ||  ||||      ||  |  |||    |||  |   ||  ||||| |   ||| ||          |||  ||||||||||||| || |||||||| |||||||| ||||||||||   | |||||  ||||||
gtttgtgtttaccattgaaa-taatatttaacaagttttcatttt---cccatttgtcttaattcatcttcttatctg---------tcttttagGAGGAAGTTGTCCTGAAGAGATGTTGGCTTGCCCGCTACTGGGGTCTTGCTGTAAAACATG

upper sequence: AT4G25070.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv17s0000g00390.t01 (Vitis vinifera), 3'ss of exon 9
gtttgcttacaatctaaactagaattttgtgcattgacggt----ttaactccaccttctttgtttcat-ttaactatatgattg-accaaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCTGTTCAACATG
                         | ||| |||  | |||    |||       ||   |  |   |   ||| | ||| | || | | |  || ||||| ||||||||||| |||||||| ||||||||||| |||||||  ||||| || || ||||
------------------------gtgtgtccataaatggtagtattagtaatgactaactgttcagacactaattgtataactgcatctatttttcagGAAGAAGTTGTTCTGAAGAGATGTTGGCTTGCTCGATACTGGGGTTTAGCCGTACATCATG

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|116426385|gb|EG468977.1|EG468977
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCCTGCTCGCTACTGGGA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
EST: gi|116426422|gb|EG469014.1|EG469014
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCT
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCT
EST: gi|116426389|gb|EG468981.1|EG468981
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
EST: gi|116426396|gb|EG468988.1|EG468988
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCT
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCT
EST: gi|116426415|gb|EG469007.1|EG469007
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCT
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCT
EST: gi|116426404|gb|EG468996.1|EG468996
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
EST: gi|116426393|gb|EG468985.1|EG468985
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
EST: gi|116426400|gb|EG468992.1|EG468992
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTCGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAA
EST: gi|116426413|gb|EG469005.1|EG469005
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCT
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCT
EST: gi|116426386|gb|EG468978.1|EG468978
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTCGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAA
EST: gi|116426401|gb|EG468993.1|EG468993
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTCGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
EST: gi|116426408|gb|EG469000.1|EG469000
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCT
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCT
EST: gi|116426402|gb|EG468994.1|EG468994
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAA
EST: gi|116426418|gb|EG469010.1|EG469010
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCT
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCT
EST: gi|116426395|gb|EG468987.1|EG468987
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTG
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTG
EST: gi|116426388|gb|EG468980.1|EG468980
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAA
EST: gi|116426391|gb|EG468983.1|EG468983
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
EST: gi|116426384|gb|EG468976.1|EG468976
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCCTGCTCGCTACTGGGAA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAA
EST: gi|116426407|gb|EG468999.1|EG468999
EST:     AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATG                         GAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA
genomic: AGTCTCTTCGGACAATGATACATAGAACGATTTTGAGTCAAGAAGAAATGgtttgcttac ... aaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttaactccaccttctttgtttcatttaactatatgattgaccaaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCTGTTCAACATG
                                     gattgac  putative branch site (score: 3)
                     tttcatttaactatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcttacaatctaaactagaattttgtgcattgacggtttaactccaccttctttgtttcatttaactatatgattgaccaaccttgcagGAGGAAGTTGTTCTAAAGAGATGCTGGCTTGCTCGCTACTGGGAATTAGCTGTTCAACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT