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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcgattctttacctggagatttttctgtgtgatgaatctctagttagggatagtttatgattttgtgggttttaagttttcagGTGGGAAGAATGGCTGGTCAGTTTGCGAAGCCGAGATCAGACCCATTTGAGGAGAAAGATGGTGTGAAGCTGCCGAGTTACAGAGGAGATAACATAAATG

Basic information

species Arabidopsis thaliana
transcript AT4G33510.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G33510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os08g37790.1 (Oryza sativa), 3'ss of exon 1
-gtcgattct-ttacctggagatttttctgtg----tgatgaatctctagttag----ggatag---tttatgattttgtgggtttta---agttttcagGTGGGAAGAATGGCTGGTCAGTTTGCGAAGCCGAGATCAGACCCATTTGAGGAGAAAGATGGTGTGAAGCTGCCGAGTTACAGAGGAGATAACATAAATG
  |   | || |||||  |   |||||  ||     | ||| || ||||||       | | ||   | ||| | ||  ||  |   |   | | |  |||| ||||||||||| ||||||||||| ||||| || |||||    ||||||||||  ||||| |||||| |||| || |||||||| |||||||| ||||
cttttctcctgttaccatgttgtttttgcgttcctttaatgcatttctagtggacatcgcacagaattgtatcacttactgtctcacatggaatatgtagGTAGGAAGAATGGCAGGTCAGTTTGCAAAGCCAAGGTCAGATGGCTTTGAGGAGAGGGATGGAGTGAAGTTGCCAAGCTACAGAGGGGATAACATTAATG

upper sequence: AT4G33510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM5G828182_T02 (Zea mays), 3'ss of exon 1
------------gtcgattctttacctggagatttttctgtgt---gatgaatctctagttagggata-gtttatgattttgtgggttttaagttttcagGTGGGAAGAATGGCTGGTCAGTTTGCGAAGCCGAGATCAGACCCATTTGAGGAGAAAGATGGTGTGAAGCTGCCGAGTTACAGAGGAGATAACATAAATG
            |        | ||   ||| |  || | | |    || |  |||||| ||        ||||   |  |        |   | |  |||||||||||||||| || |||||||||||||| || |||||    |||||||||    ||||  ||||| |||| || || ||||| || || || ||||
atgaggaattaggatatacgatcacacagagctggttgtatttctaaatcatgctctagataacttcgcatttactgtaataatatgcatggatgtctagGTGGGAAGAATGGCAGGGCAGTTTGCGAAGCCAAGGTCAGATGGTTTTGAGGAGCGGAATGGATTGAAGTTGCCAAGCTATAGAGGGGACAATATCAATG

upper sequence: AT4G33510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G06020.1 (Glycine max), 3'ss of exon 1
-----------gtcgattctttacctggagatttttctgtgtgatgaatctc----tagttagggatagt-ttatgattttgtgggttttaagttttcagGTGGGAAGAATGGCTGGTCAGTTTGCGAAGCCGAGATCAGACCCATTTGAGGAGAAAGATGGTGTGAAGCTGCCGAGTTACAGAGGAGATAACATAAATG
              ||||   ||     | || || |||  |    ||| |     | | |  ||||    || |    |||| || | |     |||||||||| |||||||| ||||| ||||| ||||||||||| ||  |||||||||||||  |||| |||| ||| ||||||||||| || |||||  | ||||
ttccattgagtaatgattagatagtctcacatattactggttttaaaattttatgatggatgaggatgacattcttcaattgttggatatggtgattcagGTGGGGAGAATGGCAGGTCAATTTGCAAAGCCGAGATCCGATTCATTTGAGGAGAAGAATGGAGTGACGCTCCCGAGTTACAGGGGTGATAATGTGAATG

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|86041190|gb|DR336945.1|DR336945
EST:     TTCAGATGGGTGTTGTTCTCATGTTCGGTGGCCAGTTACCAGTTATCAAG                         GTGGGAAGAATGGCTGGTCAGTTTGCGAAGCCGAGATCAGACCCATTTGAG
genomic: TTCAGATGGGTGTTGTTCTCATGTTCGGTGGCCAGTTACCAGTTATCAAGgtcgattctt ... aagttttcagGTGGGAAGAATGGCTGGTCAGTTTGCGAAGCCGAGATCAGACCCATTTGAG
EST: gi|124730261|gb|EH821663.1|EH821663
EST:     AGTTACCAGTTATCAA-                         GTGGGAAGAATGGCTGGTCAGTTTGCGAAGCCGAGATCAGACCCATTTGAG
genomic: AGTTACCAGTTATCAAGgtcgattctt ... aagttttcagGTGGGAAGAATGGCTGGTCAGTTTGCGAAGCCGAGATCAGACCCATTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgaatctctagttagggatagtttatgattttgtgggttttaagttttcagGTGGGAAGAATGGCTGGTCAGTTTGCGAAGCCGAGATCAGACCCATTTGAGGAGAAAGATGGTGTGAAGCTGCCGAGTTACAGAGGAGATAACATAAATG
                                                ttttc  CT-rich tract
                     atagtttatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcgattctttacctggagatttttctgtgtgatgaatctctagttagggatagtttatgattttgtgggttttaagttttcagGTGGGAAGAATGGCTGGTCAGTTTGCGAAGCCGAGATCAGACCCATTTGAGGAGAAAGATGGTGTGAAGCTGCCGAGTTACAGAGGAGATAACATAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT