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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttttataaaactgtaagacaattttctataaaaaaaatgaattccttttttttcttttcatttattgattaattaatatattgttccggcaaatcagGTGGATTGGACGCCGGAGTTACACCGGAAATTTGTACAAGCGGTGGAGCAATTAGGGGTAGACAAGGCGGTGCCGTCTCGAATCTTGGAAATTATGAACG

Basic information

species Arabidopsis thaliana
transcript AT5G44190.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G44190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g13740.2 (Oryza sativa), 3'ss of exon 1
tttttttataaaactgtaagacaattttctataaaaaaaatgaattccttttttttcttttcatttattgattaattaatatattgttccg---gcaaatcagGTGGATTGGACGCCGGAGTTACACCGGAAATTTGTACAAGCGGTGGAGCAATTAGGGGTAGACAAGGCGGTGCCGTCTCGAATCTTGGAAATTATGAACG
  |   | ||     | |     || ||  |  | |  ||| | |   | |  |||         ||| |||  ||  ||  |||| |      |     |||||||| |||||||||||||| ||||||   || || || |||||||||||  | ||| |||||||||| ||||||||  | ||| ||||  | |||  | 
--taggtgtaggcaggcacagtgatattacaagagattaattagtggatgtggttttgagaaggatatggatcgat-gatggattggtggatatgtgttgcagGTGGACTGGACGCCGGAGTTGCACCGGCGGTTCGTGCAGGCGGTGGAGCAGCTCGGGATAGACAAGGCCGTGCCGTCCAGGATCCTGGAGCTCATGGGCA

upper sequence: AT5G44190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G026833_T01 (Zea mays), 3'ss of exon 1
----------------------tttttttataaaactgtaag-acaattttctataaaaaaaatgaattc--cttttttttcttttcatttattgattaattaatatattgttccggcaaatcagGTGGATTGGACGCCGGAGTTACACCGGAAATTTGTACAAGCGGTGGAGCAATTAGGGGTAGACAAGGCGGTGCCGTCTCGAATCTTGGAAATTATGAACG
                      | |     || | |  |||   |||    ||| | | | |   ||         |  | |  | ||| | | | |    | | || |  |  |   ||  ||||||||||||||||||||| | ||||||| ||| || || ||||||||| |  | ||  | |||||||||||||||||  | ||| | || || |||    
gtacgcagggctacgcatgcagtataggcgtatagcaataattgcaaagccctaaatatatagcaaaacaaagcgatgataccatgcatgtgt-gctctgctgacatgtcttaact-taacacagGTGGATTGGACGCCGGAGCTTCACCGGAGATTCGTTCAGGCGGTGGAGGAGCTGGGCATCGACAAGGCGGTGCCGTCCAGGATCCTCGAGATCATGGGGA
















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|125186506|gb|EL201460.1|EL201460
EST:     TTGTTTATCCGATGAGAACGATATTAAGAAAAAACCTAAG                         GTGGATTGGACGCCGGAGTTACACCGGAAATTTGTACAAGCGGTGGAGCAA
genomic: TTGTTTATCCGATGAGAACGATATTAAGAAAAAACCTAAGgtgtgtttat ... ggcaaatcagGTGGATTGGACGCCGGAGTTACACCGGAAATTTGTACAAGCGGTGGAGCAA
EST: gi|124970059|gb|EL043916.1|EL043916
EST:     AAAGTAAAGATTGTTTATCCGATGAGAACGGTATTAAGAAAAAACCTAAG                         GTGGATTGGACGCCGGAGTTACACCGGAAATTTGTACAAGCGGTGGAGCAA
genomic: AAAGTAAAGATTGTTTATCCGATGAGAACGATATTAAGAAAAAACCTAAGgtgtgtttat ... ggcaaatcagGTGGATTGGACGCCGGAGTTACACCGGAAATTTGTACAAGCGGTGGAGCAA
EST: gi|125305502|gb|EL319587.1|EL319587
EST:     AAGTAAAGATTGTTTATCCGATGAGAACGATATTAAGAAAAAACCTAAAG                         GTGGATTGGACGCCGGAGTTACACCGGAAATTTGT
genomic: AAGTAAAGATTGTTTATCCGATGAGAACGATATTAAGAAAAAACCTAA-Ggtgtgtttat ... ggcaaatcagGTGGATTGGACGCCGGAGTTACACCGGAAATTTGT
EST: gi|125020705|gb|EL092974.1|EL092974
EST:     AAAGTAAAGATTGTTTATCCGATGAGAACGATATTAAGAAAAA-CCTAAG                         GTGGATTGGACGCCGGAGTTACACCGGA
genomic: AAAGTAAAGATTGTTTATCCGATGAGAACGATATTAAGAAAAAACCTAAGgtgtgtttat ... ggcaaatcagGTGGATTGGACGCCGGAGTTACACCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttttttcttttcatttattgattaattaatatattgttccggcaaatcagGTGGATTGGACGCCGGAGTTACACCGGAAATTTGTACAAGCGGTGGAGCAATTAGGGGTAGACAAGGCGGTGCCGTCTCGAATCTTGGAAATTATGAACG
                            aattaat  putative branch site (score: 3)
     ttttttcttttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttttataaaactgtaagacaattttctataaaaaaaatgaattccttttttttcttttcatttattgattaattaatatattgttccggcaaatcagGTGGATTGGACGCCGGAGTTACACCGGAAATTTGTACAAGCGGTGGAGCAATTAGGGGTAGACAAGGCGGTGCCGTCTCGAATCTTGGAAATTATGAACG

- - - -ataaaac
- - - - - - - - -aagacaa
- - - - - - - - - - - - - - - - aaaaaaa