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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattttgatgtctgtgttgccataacagcttttatgtcatcttatgcaattttgatctcataagctatctgttcttactcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC

Basic information

species Arabidopsis thaliana
transcript AT1G06890.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 2
-cattttgatgtctgtgttgcca--taacagcttttatgtcatcttatgcaattttgatctcataagctatctgttcttactcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
   ||||      ||  |||| |  ||  ||  ||| |   || |     ||| |  ||  ||  | || | | | | |||   ||  ||| | | | | |||| ||||| ||||| |||||||||||| | ||||||||||| ||||| ||||| ||||||||||||||| | ||||| ||||||||||| ||  |  || |
ttcttttctcaaatgcattgcaatgtattagtgtttgtagaatttacatgaatataaatgacaccaactgtttttccataca--tggaattgtattt-tgcagCCACTACCTTGACGAGTTGGCATCTTCTTGTCACATTTTGCTCCCTCCATGTAGCATTATGGATGAAGTTCTTCGAGCACAAGCCTTTCGACTCGAGAAC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
cattttgatgtctgtgttgccataacagcttttatgtcatctta-tgcaattttgatctcataagctatctgttcttactcttgttattttgtatgt-acagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
  || | | || ||||   | |||  || |    |   |  ||| | ||    |   |   |   || ||     |        |   | ||| | |  |||| |||||||||||||| ||||||||  | || |||||||| || ||||| ||||||||||| |||||| | || || ||||| ||||||||| || |  |
ggttctaaagtgtgtg--acaatactaggtaacgtaaaaagttagtacataaatagacgtgtttcctgtccaaattactcaacttcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g60780.2 (Oryza sativa), 3'ss of exon 1
cattttgatgtctgtgttgcca-taacagcttttatgtcatcttatgcaattttgatct-cataagctatctgttcttactcttgttattttgtatgta-cagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
   | |||   |  | |  | |  || | |   |  |  | || |     |  | | ||  |||| |   |     | ||     |    |  | | |  |||| |||||  ||||||| ||||||||  |||| |||||||||||||||||||||||  |   ||||||| | |||||  ||||   ||| || ||     |
---tatgagtacaatatgacgaacaataccacctgagaaaactaactgtttcctaagctatataaccatgcaaaaatcacagcactctcctaatttctttcagCTACTACGCTGACAAGCTGGCATCTCCTGGTGACATTTTGTTCCCTTCATGTGGCTCTTCAGATGAAGCTTTTCGAGAACAAAGATTTAGACCCCAAGAC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 2
------cattttgatgtctgtgttgccataa-cagctttt-atgtcatcttatgcaattttgatctcataagctatctgttcttactcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
         |  | || | |||   | |||| ||| |  | ||  ||    | |||  |||     ||   | ||        |  | ||   ||||||      |||| |||||||||||||| ||||||||  |||| ||||| ||||| || |||||||||||||| |||||| |||| || ||||| ||||| ||| || |  |
caagtgtggtgaggtgacagtgcgtctataaacagataatgatagcaaagaaggcaggttttcctccaagtgttaataaaatgtggtatt--cattttg------cagCCACTACTTTGACAAGCTGGCATCTCCTGGTTACATTCTGTTCTCTCCATGTGGCATTATGTATGAAGCTGTTTGAGCACAAACCTTTCGATGCAAGGAC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 2
-cattttgatgtctgtgttgccataacagcttttatgtca-tcttatgcaattttgatctcataagctatctgttcttactcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
 ||      |   | | |   |||         ||||  | ||| ||  || | |  ||| ||   ||||  ||| | |    ||| ||||    | | |||| ||||| |||||||| ||||||||  |||| ||||| || ||||||||||||||||||||||||||  | || || || |||||||||||| || || |
acacgccccttattttatcaacatgtggtggagtatgcaagtctgatttaaatgtcttcttatggactatg-gttgtgaaatatgt-atttgtcttctgcagCCACTACCTTGACAAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTGGCATTATGGATGAAATTCTTTGAGCATAAGCCTTTTGATTCAAGAAC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G063253_T09 (Zea mays), 3'ss of exon 1
cattttgatgtctgtgttgccataacagcttttatgtcatcttatgcaattttgatctcataagctatctgttcttactcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
||   |  |   | |  |   || |     | | |       |||| || | |||| | |    ||     |   |        | | |    | | |||| ||||| ||||| || ||||||||  |||| ||||| || ||||||||||| ||||||||||||||| | || || || |||||||||||| || || |
cagagtactagatcttatattatcaacatgtatgtagtgaagtatgtaagtctgatttaaatgacttctaatatctgtgaaatatgtatgtcttttgcagCCACTACCTTGACGAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTAGCATTATGGATGAAGTTCTTTGAGCATAAGCCTTTTGATTCAAGAAC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 1
cattttgatgtctgtgttgccataacagcttttatgtcatcttatgcaattttgatctcataagctatctgttcttactcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
                              | | |       |||| || | |||| | |    ||     |   |        | | |    | | |||| ||||| ||||| || ||||||||  |||| ||||| || ||||||||||| ||||||||||||||| | || || || |||||||||||| || || |
-----------------------------gtatgtagtgaagtatgtaagtctgatttaaatgacttctaatatctgtgaaatatgtatgtcttttgcagCCACTACCTTGACGAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTAGCATTATGGATGAAGTTCTTTGAGCATAAGCCTTTTGATTCAAGAAC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 2
------cattttgatgtctgtgttgccataa-cagcttttat-gtcatcttatgcaattttgatctcataagctatctgttcttactcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
         |    || | ||    | |||| ||| |  |||   ||    | |||  |||     |||| ||||        |  | ||   ||||||      |||| || ||||||||||| ||||||||| ||||||| || || || || ||||| |||||||| |||||  | || || ||||| ||||| ||| || |  |
cacgtgtcctcaagtgacagtccgtctataaacagataatattagcaaagaaggcaggttttcctccatatgctaataaaatctcgtatt--cattttg------cagCCACCACTTTGACAAGCTGGCATCTTCTGGTCACCTTCTGCTCTCTCCATGTAGCATTATGTATGAAACTCTTTGAGCACAAACCTTTCGATGCAAGGAC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
--cattttgatgtctgtgttgccataacagcttttatgtcatcttatgcaattttgatctcataagctatctgttcttactcttgttattttgta--tgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
    ||||| |    ||    ||||      |  ||   ||| | | | |    | || || ||   |    ||| | |    | |  ||   |     | |||| || ||||||||||||||||||||| | || |||||||||||||||||||||||| ||  | |||   | || || ||||| |||||||| |    |||
taacttttgttagaagtagctccatgctgcatcctaacccatttgaagta----taatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 2
-cattttgatgtctgtgttgccataacagcttttatgtcatcttatgcaattttgatctcataagctatctgttctt-actcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
  ||||  |||  | | |    ||   |||||| ||||   | | |  |  |    ||| |  |  ||   ||| || |   ||||  ||||  || | |||| || |||||||| || ||||||||  | ||||||||||||||||||||||||||  |    ||||   | || || ||||| |||||||| |    |||
ttatttccatga-tatatgcaaatttgagctttcatgtttacattttaatgtactgtctga-gatttacaagtttttgaaatttgtgctttttgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACATTTTGTTCCCTTCATGTGGCGCTCAAAATGAGATTCTTTGAGCACAAACCTTTTGAGCAGAAAGC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G39920.4 (Glycine max), 3'ss of exon 2
-cattttgatgtctgtgttgccataacagcttttatgtcatcttatgcaattttgatctcataagctatctgttctt-actcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
  || || ||| || | |    ||   |||||| || |   | | |  |  |    ||| |  |  ||   ||| || |   ||||  ||||  || | |||| || |||||||| || ||||||||  | ||||| ||||||||||||||||||||  |    ||||   | || || ||||| |||||||| |    |||
ttatgttcatg-ctatatgcaaatttgagctttcatctttacattttaatgtactgtctga-gatttacaagtttttgaaatttgtgctttttgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATGTGGCGCTCAAAATGAGATTCTTTGAGCACAAACCTTTTGAGCAGAAAGC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
---cattttgatgtctgtgttgccataacagcttttatgtcatct--tatgcaattttgatctcataagctatctgttcttactcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
    |      |  ||   ||   |||   ||| || |  || ||  | ||  | |||  |||  | || | ||  || | |||      | | |  || | |||| || ||||| || || ||||||||| |||||||||||||||| |||||||||||| ||||||||||  | || || ||||||||||||||  |  ||||
agtgaaaacttttcctccattcatatatttgctcttttcacagctgctttgttaatttagtct--tgagttctc-attttaactacc-caactgtcgat-tgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC

upper sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
-cattttgatgtctgtgttgccataacagcttttatgtcatcttatgcaattttgatctcataagctatctgttcttactcttgttattt-tgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
 |  || |  |        ||  ||||     | ||   ||  | ||  ||     |  | |   ||    |   |  ||  ||| ||   | | |||||||| ||||| |||||||| ||||||||| ||||||| || ||||| |||||||||||  ||||||||||  |||| |||||||| || |||||| ||  |||
gctattaggcggtaacaaagcactaactataatgattgtatactttg--ataagatttgcttctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC

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|125326527|gb|EL340607.1|EL340607
EST:     GATTGTGATCTGTAACAAAGCGCTTATTAGCACCCTTGGCTTCACATTCG                         CGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCA
genomic: GATTGTGATCTGTAACAAAGCGCTTATTAGCACCCTTGGCTTCACATTCGgtaacctttt ... gtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaattttgatctcataagctatctgttcttactcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC
                          ttcttac  putative branch site (score: 2)
                                   ttgttattttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattttgatgtctgtgttgccataacagcttttatgtcatcttatgcaattttgatctcataagctatctgttcttactcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - cataaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataagc