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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcaatcatttgagatcttagttagagtagtatatttgagacaccctcttgattcttgagttcttgttataacaattttgtatcttttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGTGATTACATGCCAATTGCCAGTGTCAAGGCAGCTATGGAGCTAGTTAAGC

Basic information

species Arabidopsis thaliana
transcript AT5G23900.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G145280_T02 (Zea mays), 3'ss of exon 4
------------gtatcaatcatttgagatcttagttagagtagtatatttgagacaccctctt-gattcttgagttcttgttataacaattttgtatcttttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGTGATTACATGCCAATTGCCAGTGTCAAGGCAGCTATGGAGCTAGTTAAGC
            | | ||||| |||     |||||| | || | | |  ||     | |  ||| ||    | |  |||| | |             |  |||  || ||||||||||| ||||||||||||||||||||||  ||||| || || || ||||| ||||||||| || |  |||   ||  |  |   |     |||  | 
gttaaggtatgggcagcaatctttt----ccttagtgaaagcattgttcttatcttagctgcttcgacctctaatctcttatcacc-----------tactttcattgcagGCTGGTGACTCTACTCCAGAGGAGCTTGCCACCGCTACCCAGGTCCAGGGTGACTACATGCCATTTACTCGTGGTGAGAAACGTTCAGTTGAGGTTGTGA

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G145280_T01 (Zea mays), 3'ss of exon 4
------gtatcaatcatttgagatcttagttagagtagtatatttgagacaccctctt-gattcttgagttcttgttataacaattttgtatcttttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGTGATTACATGCCAATTGCCAGTGTCAAGGCAGCTATGGAGCTAGTTAAGC
      | | ||||| |||     |||||| | || | | |  ||     | |  ||| ||    | |  |||| | |             |  |||  || ||||||||||| ||||||||||||||||||||||  ||||| || || || ||||| ||||||||| || |  |||   ||  |  |   |     |||  | 
gtatgggcagcaatctttt----ccttagtgaaagcattgttcttatcttagctgcttcgacctctaatctcttatcacc-----------tactttcattgcagGCTGGTGACTCTACTCCAGAGGAGCTTGCCACCGCTACCCAGGTCCAGGGTGACTACATGCCATTTACTCGTGGTGAGAAACGTTCAGTTGAGGTTGTGA

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G081102_T03 (Zea mays), 3'ss of exon 4
gtatcaatcatt-tgagatcttagttagagtagtatatttgagacaccctcttgattcttgagttcttgttataacaattttgtatct--tttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGTGATTACATGCCAATTGC---CAGTGTCAAGGCAGCTATGGAGCTAGTTAAGC
|||| | |  |  |    || |    |    ||||| | |   |  |  | |   |   ||  ||  | | | ||    ||   | ||  |||  || ||||||||||| |||||||  ||||||||| ||| |||||| || || || ||||| |||||||||||| |   | |||  |||    || | ||| | || |   
gtatgagtagtcatcttttcctgaacaattaagtatctcttgaaggcattgtctctggctgctttgatctcaaaatcccttatcacctacttttgttgcagGCTGGTGACTCTACTCTGGAGGAGCTTACCACTGCTACCCAGGTACAGGGTGACTACATGCCAATTACTCGCGGTGAGAAGCGCTCTGTAGAGGTTGTGA---

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G34760.2 (Glycine max), 3'ss of exon 4
-------------gtatcaatcatttgagatcttagttagagtag-----tatatttgagacaccctcttgattcttgagttcttgt-tataacaattttgtatcttttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGTGATTACATGCCAATTGCCAGTGTCAAGGCAGCTATGGAGCTAGTTAAGC
               ||    ||||    || ||  ||   ||||     |  ||||  ||       |  | |      |  |||| | | |        | |  |||  ||  ||||||||||||||||||| ||||||||||| ||||| || ||||| || |||| || | |||| ||||  || |  ||| || || | || || || ||| 
gttaaggtaattcagatgttccattatctattttgattgtggtaggcattttcatttctgatgaaggttgaaatgaaagatgtttgtgtgtcatgtgacactgttgttttattgtagGCTGGTGATTCTACTCCCGAGGAGCTTGCAAATGCAACACAAGTCCAGGGTGCTTTCTTGCCTATTGTGAGGGAGAAGCCAACTGTTGAACTTGTAAAGG

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G14640.2 (Glycine max), 3'ss of exon 4
-----------------------gtatcaatcatttgag----atcttagttagagtagtat-atttgagacaccctcttgattcttgagttcttgttataacaattttgtatcttttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGTGATTACATGCCAATTGCCAGTGTCAAGGCAGCTATGGAGCTAGTTAAGC
                       || |  ||  | || |     ||||| ||    ||  || ||||  |        |  |       | | ||  | | | |  |   | |  |||  ||  ||||||||||||||||||| ||||||||||| ||||| || ||||| || |||  || | |||| ||||  || |  ||| || || | || || || ||| 
gtaatacagatgttcaattatctgttttgattgtgtgggcattgtcttaattttgatatcatcatttctggtgaaaggtaaaaaggaatgatgtttgtgtgaaatctgactgttgttttattgtagGCTGGTGATTCTACTCCCGAGGAGCTTGCAAATGCAACGCAAGTCCAGGGTTCTTTCTTGCCTATTGTGAGGGAGAAGCCAACTGTTGAACTTGTAAAGG

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 5
-------gtatcaatcatttgagatcttagttagagtag-----tatatttgagacaccctcttgattcttgagttcttgt-tataacaattttgtatcttttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGTGATTACATGCCAATTGCCAGTGTCAAGGCAGCTATGGAGCTAGTTAAGC
         ||    ||||    || ||  ||   ||||     |  ||||  ||       |  | |      |  |||| | | |        | |  |||  ||  ||||||||||||||||||| ||||||||||| ||||| || ||||| || |||| || | |||| ||||  || |  ||| || || | || || || ||| 
gtaattcagatgttccattatctattttgattgtggtaggcattttcatttctgatgaaggttgaaatgaaagatgtttgtgtgtcatgtgacactgttgttttattgtagGCTGGTGATTCTACTCCCGAGGAGCTTGCAAATGCAACACAAGTCCAGGGTGCTTTCTTGCCTATTGTGAGGGAGAAGCCAACTGTTGAACTTGTAAAGG

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G08090.1 (Glycine max), 3'ss of exon 4
-------------------gtatcaatcatttgagatcttagttagagtagtat--atttgaga-----caccctcttgattcttgagt----tcttg----ttataacaattt-tgtatct-tttgtttt-cagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGTGATTACATGCCAATTGCCAGTGTCAAGGCAGCTATGGAGCTAGTTAAGC
                    ||| | | ||||||    |  ||   | |  |||  |||| |       ||  | ||||    | |       | |||    ||   |   ||| |||  || |||| ||| ||||||||||||||||| || || ||||| || ||||| ||||||||||| |||   | | |||| ||||  || |  ||| || || | || || |||||| 
gtaaagctaaattcttcaattattattaatttgatggttatgtgcaaattttatttattttatggtcatcattcccttggaagtaggaaacaatattgaagtttgagattgtttatgtccctatttgctttgcagGCTGGTGATTCTACCCCTGAAGAGCTGGCTAATGCCACTCAAGTTCAGGGTTCATTCTTGCCCATTGTGAGGGAGAAGCCAACTGTTGACCTTGTTAAGG

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|164230820|gb|ES093144.1|ES093144
EST:     CCTCGCCGTTCCCGCCAAGTCAAG                         GCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGT
genomic: CCTCGCCGTTCCCGTCAAGTCAAGgtatcaatca ... ttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGT
EST: gi|124704010|gb|EH795412.1|EH795412
EST:     CTTACAAGGCTAAGTTGGTGGTGTTCCCTCGCCGTTCCCGTCAAGTCAAG                         GCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCT
genomic: CTTACAAGGCTAAGTTGGTGGTGTTCCCTCGCCGTTCCCGTCAAGTCAAGgtatcaatca ... ttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCT
EST: gi|125177960|gb|EL196713.1|EL196713
EST:     GCTAAGTTGGTGGTGTT-CCTCGCCGTTCCCGTCAAGTCAAG                         GCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGT
genomic: GCTAAGTTGGTGGTGTTCCCTCGCCGTTCCCGTCAAGTCAAGgtatcaatca ... ttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGT
EST: gi|47830737|gb|CK120421.1|CK120421
EST:     CTTACAAGGCTAAGTTGGTGGTGTTCCCTCGCCGTTCCCGTCAAGTCAAG                         GCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGT
genomic: CTTACAAGGCTAAGTTGGTGGTGTTCCCTCGCCGTTCCCGTCAAGTCAAGgtatcaatca ... ttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGT
EST: gi|164213384|gb|ES016707.1|ES016707
EST:     CTTACAAGGCTAAGTTGGTGGTGTTCCCTCGCCGTTCCCGTCAAGTCAAG                         GCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTC
genomic: CTTACAAGGCTAAGTTGGTGGTGTTCCCTCGCCGTTCCCGTCAAGTCAAGgtatcaatca ... ttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTC
EST: gi|164035981|gb|ES211202.1|ES211202
EST:     TGGTGTTCCCTCGCCGTTCCCGTCAAGTCAAG                         GCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGT
genomic: TGGTGTTCCCTCGCCGTTCCCGTCAAGTCAAGgtatcaatca ... ttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccctcttgattcttgagttcttgttataacaattttgtatcttttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGTGATTACATGCCAATTGCCAGTGTCAAGGCAGCTATGGAGCTAGTTAAGC
                         ttataac  putative branch site (score: 2)
                                       tatcttttgttttc  putative PPT
                         ttataacaattttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcaatcatttgagatcttagttagagtagtatatttgagacaccctcttgattcttgagttcttgttataacaattttgtatcttttgttttcagGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGTGATTACATGCCAATTGCCAGTGTCAAGGCAGCTATGGAGCTAGTTAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT