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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgataaaacatttcctgcaaaagtttaacgttgactagtagtatctgatatgccatgttttcttagatgtaatggttatattttgtcttttactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAGGGTTCCCTCCCGAAGCTAATTATTTGTTCTTGGGTGATTATGTTGACCG

Basic information

species Arabidopsis thaliana
transcript AT2G29400.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G29400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g16110.1 (Oryza sativa), 3'ss of exon 1
--tgataaaacatttcctgcaaaagtttaacgttgactagtagtatctgatatgccatgttttcttagatgtaatggttatattttgtcttttactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAGGGTTCCCTCCCGAAGCTAATTATTTGTTCTTGGGTGATTATGTTGACCG
  |  |      ||||   |   |||    |  | | |  | ||| ||| |    |     |   ||  |    |  || |   ||||| |||  | |  |||||| || ||||| |||||    || ||  | ||||||||||||||||| || || || || ||||| |||||| | ||||| |||||||||||||| ||
cttcttggggagtttcaatctgtagtgagcctgtaaat--ttgtagctggtggctctaaggtgtgtatttaacttttttttcacttgtcatttggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTGGTTTTCCCCCAGAAGCCAATTATCTATTCTTAGGTGATTATGTTGATCG

upper sequence: AT2G29400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G160237_T02 (Zea mays), 3'ss of exon 2
tgataaaacatttcctg-caaaagtttaacgttgactagtagtatctgatatgccatgttttcttag-atgtaatggttatattt--tgtcttttactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAGGGTTCCCTCCCGAAGCTAATTATTTGTTCTTGGGTGATTATGTTGACCG
   |   |  ||| |||   |||| ||     ||  |  | || | |  | || | |  ||   ||| || |||  |  || |    |||| |||  | |  |||||| || ||||| || ||    |||||  | ||||||||||| |||||||| || ||||| ||||| |||||| | ||||| |||||||||||||| ||
--tttctatttttactgatgaaagctttggactg--tgattgtgtgtcctttgtcttcattgaatagtatctaagtgcaatctccactgtcatttggtatccagGTGACATCCATGGTCAATACAGTGATCTTCTAAGGCTTTTTGAATATGGAGGCTTTCCTCCTGAAGCCAATTATCTATTCTTAGGTGATTATGTTGATCG

upper sequence: AT2G29400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 1
-tgataaaacatttcctgcaaaagtttaacgt--tgactagtagtatctgatatgccatgttttcttagatgtaatggttatattttgtcttttactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAGGGTTCCCTCCCGAAGCTAATTATTTGTTCTTGGGTGATTATGTTGACCG
 |         |||  ||     |||  | |   |  | | | |    |  | ||  || || | ||   | | | |   | |||||    ||    |  ||||||| || || || ||||| || ||||| ||||| || ||||||||||| || || |||||||| || || || |||||| ||||||| |||||||| ||
ttttgcccgtgtttagtgtctttgttctatggcatagccacttgctctttgtctgaaat-ttcttttgtttctcacgagaagatttt--tcttcgtgtgctagGTGACATCCACGGCCAGTACTCGGATCTCTTGAGACTGTTTGAGTATGGTGGCTTTCCTCCCGAGGCCAACTACTTGTTCCTGGGTGACTATGTTGATCG

upper sequence: AT2G29400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ20637 (Selaginella moellendorffii), 3'ss of exon 1
-tgataaaacatttcctgcaaaagtttaacgt--tgactagtagtatctgatatgccatgttttcttagatgtaatggttatattttgtcttttactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAGGGTTCCCTCCCGAAGCTAATTATTTGTTCTTGGGTGATTATGTTGACCG
 |         |||  ||     |||  | |   |  | | | |    |  | ||  || || | |    | | | |   | |||||    ||    |  ||||||| || || || ||||| || ||||| ||||| || ||||||||||| || || |||||||| || || || |||||| ||||||| |||||||| ||
ttttgcccgtgtttattgtctttgttctatggcatagccacttgctctttgtctgaaat-ttctttggtttctcacgagaagatttt--tcttcgtgtgctagGTGACATCCACGGCCAGTACTCGGATCTCTTGAGACTGTTTGAGTATGGTGGCTTTCCTCCCGAGGCCAACTACTTGTTCCTGGGTGACTATGTTGATCG

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|86065903|gb|DR361660.1|DR361660
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         G--ATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065915|gb|DR361672.1|DR361672
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065908|gb|DR361665.1|DR361665
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065905|gb|DR361662.1|DR361662
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGNATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065918|gb|DR361675.1|DR361675
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065899|gb|DR361656.1|DR361656
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065904|gb|DR361661.1|DR361661
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065910|gb|DR361667.1|DR361667
EST:     TCTTCAAAAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065907|gb|DR361664.1|DR361664
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GNGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065917|gb|DR361674.1|DR361674
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|301502680|gb|HO208220.1|HO208220
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065913|gb|DR361670.1|DR361670
EST:     TCTTNAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCNAGATCTGCG                         GNGATATTCATGGGCAGGATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065900|gb|DR361657.1|DR361657
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GNGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065906|gb|DR361663.1|DR361663
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|86065914|gb|DR361671.1|DR361671
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
EST: gi|116434806|gb|EG477398.1|EG477398
EST:     TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCG                         GTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG
genomic: TCTTCAACAGCCCAATCTGCTTGAATTGGAAGCTCCCATCAAGATCTGCGgtcagatttt ... tactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatatgccatgttttcttagatgtaatggttatattttgtcttttactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAGGGTTCCCTCCCGAAGCTAATTATTTGTTCTTGGGTGATTATGTTGACCG
 atctgat  putative branch site (score: 4)
                                   ttttgtcttttacttt  putative PPT
                              ttatattttgtctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgataaaacatttcctgcaaaagtttaacgttgactagtagtatctgatatgccatgttttcttagatgtaatggttatattttgtcttttactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAGGGTTCCCTCCCGAAGCTAATTATTTGTTCTTGGGTGATTATGTTGACCG

- -taaaaca
- - - - - - - - gcaaaag