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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaatggtggttacttactgttactatgattaaatgcttttgaaaagttttgatatttctcaataaatgatgatacttttttttatggttgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG

Basic information

species Arabidopsis thaliana
transcript AT3G50500.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G171435_T01 (Zea mays), 3'ss of exon 1
------tttaatggtggttacttactgttactatgattaaatgcttttgaaaagttttgatatttctcaataaatgatgatacttttttttatggttgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG
      ||  ||  |   | ||    ||||  ||   | |||   |      | ||  | | | ||    |      | ||| |   ||| ||  |  ||| |||||| ||||| ||||| ||| | || || || || ||||||||||||| ||| ||||| ||| ||||||||||||||
tgcattttctatcataaatgctag--gttatcatttcttaattaatacactcaatt--gctttgtcaaggttttctttaata-tggatttcattatcattt-gcagATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACACCCTAACATTATTAGGTTTAAAGAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 2
tttaatggtggttacttactgttactatgattaaatgcttt--tgaaaagttttgatatttctcaataaatgatgatacttttttttatggttgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG
  |  |  |  |   | |    | ||| | |   ||  |||  || |     ||| | | |||   |      | ||| | | ||   | ||  | | |||||| ||||| ||||| ||| | ||||| || || |||||||||||||  || ||||| ||| ||||||||||||||
cattttcttcttctatcataagtgctaggttgtcattttttactgcactcagttgttttatcttggttttctttaata-tgtattccgttgtcatgt-gcagATAGATGAGAATGTCCAGCGTGAGATAATTAACCATAGATCATTGAAGCACCCTAACATTATTAGGTTTAAAGAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G138861_T02 (Zea mays), 3'ss of exon 1
tttaatggtggttacttactgttactatgattaaatgcttttgaaaagtt--ttgatatttctcaataaatgatgatacttttttttatggttgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG-------------------------
  |  |  |  |   | |    | ||| | |   ||  |||     | |   ||| | | |||   |      | ||| | | ||   | ||  | | |||||| ||||| ||||| ||| | ||||| || || |||||||||||||  || ||||| ||| ||||||||||||||                         
cattttcttcttctatcataagtgctaggttgtcattttttactgcactcagttgttttatcttggttttctttaata-tgtattccgttgtcatgt-gcagATAGATGAGAATGTCCAGCGTGAGATAATTAACCATAGATCATTGAAGCACCCTAACATTATTAGGTTTAAAGAGGTGAGTTGGGATTGTGATGCTGTTT

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 1
--tttaatggtggttacttact-gttactatgattaaatgcttttgaaaagttttgatatttctcaataaatgatgatacttttttttatggtt--gttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG
  |||  | |   ||  || ||     |  |  ||   || || | |     | ||||     |   | | ||||  |  || | | | | |||  || | ||||||||||||||||||  ||||||| ||||||||||| || ||  |||| |||||||| ||||||||||||||||||
ctttttttagaatttttttccttacggcattcgtttggtgtttctta----ctctgatgaagtt-gctgactgattttttttgtgtgtgttgttttgtctcgcagATTGATGAAAATGTGAAGAGGGAAATTATCAATCACAGGTCTCTGAGGCATCCTAACATTGTTAGGTTTAAAGAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 1
------tttaatggtggttacttactgttactatgattaaatgcttttgaaaagttttgatatttctcaataaatgatgatacttttttttatggttgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG
      ||| | ||   |   || |||||| | |  |   |  ||  ||||     ||  | ||| |   |   |  |  |   |  | || | || || | ||||||||||||||||||  ||||||| || || ||||| || ||  |||| |||||||| |||||||| |||||||||
gcaattttttacggcattggtttgctgttagtttctt---actctgatgaagttgcttactgttttttttttttt--ttgtgtatggtgttgttgt-gtgtcgcagATTGATGAAAATGTAAAGAGGGAAATCATTAATCACAGGTCTCTGAGGCATCCTAACATTGTTAGATTTAAAGAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G20610.3 (Glycine max), 3'ss of exon 1
------tttaatggtggttacttactgttactatgattaaatgcttttgaaaagttttgatatttctcaataaatgatgatacttttttttatggttgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG-------------------------
      ||| | ||   |   || |||||| | |  |   |  ||  ||||     ||  | ||| |   |   |  |  |   |  | || | || || | ||||||||||||||||||  ||||||| || || ||||| || ||  |||| |||||||| |||||||| |||||||||                         
gcaattttttacggcattggtttgctgttagtttctt---actctgatgaagttgcttactgttttttttttttt--ttgtgtatggtgttgttgt-gtgtcgcagATTGATGAAAATGTAAAGAGGGAAATCATTAATCACAGGTCTCTGAGGCATCCTAACATTGTTAGATTTAAAGAGGTTGGTTATGTTTTTCAAATATTTA

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 1
tttaatggtggttacttactgttactatgattaaat--gcttttgaaaagttttgatatttctcaataaatgatgatacttttttttatggttgttt--tgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG
  | | |    ||       | ||  ||    |  |  | | || ||   | |  |||| | | |  |||||  |||   |  || ||   || |||  |||||||||||||||||||||| ||||| || || |||||||| ||  | || || || || ||||||||||||||||||
--tgaagccaatttagataggctatgatatccaccttggttatttaattttatgaatatgtttta--aaatgtggatttctcattataatattctttgttgcagATTGATGAAAATGTTCAAAGGGAAATAATTAATCATAGGTCTCTCAGGCACCCCAACATTGTTAGGTTTAAAGAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 3'ss of exon 1
tttaatggtggttacttactgttactatgattaaatgctttt------gaaaagttttgatatttctcaa--taaatgatgatacttttttttatggttgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG
    |  | | |||  |  ||  | | |   | | | ||  |      |  | |||||||     |  ||  ||  | |||  |  || ||| |   ||||  |||||||||| || ||||||||| |||||||||| |||||| | || ||| | ||||| || || ||  |||| || |||
----agcgagattatatcttgggattctacgtgagtactggtagtagcgggaggttttgagtggacagaagttagctaatgtgaaattgtttga--attgt--tgcagATTGACGAGAATGTTCAGCGGGAGATTATTAATCATCGGTCGTTGCGGCATCCCAACATAGTGCGGTTCAAGGAG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 1
-----tttaatggtggttacttactgttactatgattaaatgcttttgaaaagttttgatatttctcaataaatgatgatacttttttttatggttgtttt-gcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG
     | ||||  ||    |||    |    ||| | || || | |   ||   ||||| ||||  |||    || ||||      |  |  | || |||| ||||||||| |||||||| ||| ||||||| ||||| ||| |||| ||| | ||||| || || ||  | ||| | |||
tgaggtctaatc-tgagggcttgacttggacatggt-aagtggtgtgagaa---tttga-attttgcaaagggtgctgatgtggaatggtgcgattatttttgcagATTGACGAAAATGTCCAGCGGGAGATCATCAACCATCGATCGTTGCGGCATCCCAACATAGTGCGATTTCAGGAG

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|152038572|gb|AV831382.2|AV831382
EST:     GAGTCACCAAGGAGCTTGTTGCTGTTAAATACATCGAGAGAGGAGAAAAG                         ATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACNT
genomic: GAGTCACCAAGGAGCTTGTTGCTGTTAAATACATCGAGAGAGGAGAAAAGgtttcgtctt ... tgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACAT
EST: gi|116437303|gb|EG479895.1|EG479895
EST:     GAGTCACCAAGGAGCTTGTTGCCGTTAAATACATCGAGAGAGGAGAAAAG                         ATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACAT
genomic: GAGTCACCAAGGAGCTTGTTGCTGTTAAATACATCGAGAGAGGAGAAAAGgtttcgtctt ... tgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACAT
EST: gi|164228801|gb|ES046588.1|ES046588
EST:     TACATCGAGAGAGGAGAAAAG                         ATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACAT
genomic: TACATCGAGAGAGGAGAAAAGgtttcgtctt ... tgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACAT
EST: gi|116437302|gb|EG479894.1|EG479894
EST:     GAGTCACCAAGGAGCTTGTTGCTGTTAAATACATCGAGAGAGGAGAAAAG                         ATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACAT
genomic: GAGTCACCAAGGAGCTTGTTGCTGTTAAATACATCGAGAGAGGAGAAAAGgtttcgtctt ... tgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACAT
EST: gi|116437296|gb|EG479888.1|EG479888
EST:     GAGTCACCAAGGAGCTTGTTGCTGTTAAATACATCGAGAGAGGAGAAAAG                         ATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACAT
genomic: GAGTCACCAAGGAGCTTGTTGCTGTTAAATACATCGAGAGAGGAGAAAAGgtttcgtctt ... tgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttttgatatttctcaataaatgatgatacttttttttatggttgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG
   ttttgat  putative branch site (score: 4)
                                            ttgtttt  putative PPT
        atatttctcaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaatggtggttacttactgttactatgattaaatgcttttgaaaagttttgatatttctcaataaatgatgatacttttttttatggttgttttgcagATTGATGAAAATGTTCAGAGGGAGATTATCAATCATAGATCATTGAGACATCCTAATATTGTTAGGTTTAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - ctgttac
- - - - - - - - - - - - - - - - - - gcttttg
- - - - - - - - - - - - - - - - - - - - - - - -gttttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caataaa