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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttaggcgttttagtatctcgcattctaaatttataggctaataatattcagtcgttttttaagatcagattactcttttacgttgcagGTTAAATGTTTGATGCGTCAGTTGATATCTGGTTTGGAGCATTGTCATAGTCGTGGTGTACTTCATCGTGACATCAAAGGATCAAATCTTCTTATTGATG

Basic information

species Arabidopsis thaliana
transcript AT1G54610.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 2
-----gttagttaggcgttttagtatctcgcattctaaatttataggctaataatattc------agtcgttttttaagatcag-attactct-tttacgttgcagGTTAAATGTTTGATGCGTCAGTTGATATCTGGTTTGGAGCATTGTCATAGTCGTGGTGTACTTCATCGTGACATCAAAGGATCAAATCTTCTTATTGATG
      | || |  || ||  | |  || | ||  |    | || ||   ||  | ||       ||| |  ||| | |  |   | |||| |   | | ||||||||||||||||  |||| |||| || |||| ||  | ||||| |||||||  |||  ||||||||| ||||| || |||||||||||||||||||||||  
gttagatcaggtttgccttaaaattacttgtatcatttggtaattggtacattttcttttcaaggagtaggatttgatgtcccctaatactgtgccttcattgcagGTTAAATGTTACATGCATCAGCTGTTATCAGGACTTGAGCACTGTCATAACCGTCATGTACTTCACCGTGATATTAAAGGATCAAATCTTCTTATTGACA

upper sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 2
-----gttagttaggcgttttagtatctcgcattctaaatttataggctaataatattc---agtcgttttttaaga-tcagattactcttttacgttgcagGTTAAATGTTTGATGCGTCAGTTGATATCTGGTTTGGAGCATTGTCATAGTCGTGGTGTACTTCATCGTGACATCAAAGGATCAAATCTTCTTATTGATG
      | || |  || ||  | |  || | ||  |    | || ||   ||  | ||    ||| |  ||| | |  ||  | |||| | || | |||||||| |||||||  |||| |||| || |||| ||  | ||||| |||||||  ||| |||||||||| ||||| || |||||||||||||||||||||||  
gttagatcaggtttgccttaaaattacttgtatcatttggtaattggtacattttcttttcgagtaggatttgatgtctccaaatactgtctt-cattgcagGTAAAATGTTACATGCATCAGCTGCTATCAGGACTTGAGCACTGTCATAACCGTCGTGTACTTCACCGTGATATTAAAGGATCAAATCTTCTTATTGACA

upper sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G30030.1 (Glycine max), 3'ss of exon 2
gttag-ttaggc---gttttagtatctcgcattctaaa-----tttataggctaataatattcagtcgttttttaagat----cagattac-tcttttacgttgcagGTTAAATGTTTGATGCGTCAGTTGATATCTGGTTTGGAGCATTGTCATAGTCGTGGTGTACTTCATCGTGACATCAAAGGATCAAATCTTCTTATTGATG
|||||   |||    | || |  ||||   |    |||     | | | |  |  |   | |  |  || | | | |       | ||||  |   |     |||||||||||||||  || | |||  || |||| ||  | ||||| |||||||||||    |||||||| ||||| || ||||||||||| |||||||||||  
gttaggccaggtttggcttaataatctaagaaataaaagatactctttggtttcttttcaattggctgtatgtgatgtctccatatattatatgcctcctactgcagGTTAAATGTTACATACATCAACTGCTATCAGGACTTGAGCACTGTCATAGTCGAAACGTACTTCACCGTGATATTAAAGGATCAAACCTTCTTATTGACA

upper sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 5
----------gttagttaggcgttttagt--atctcgcatt--ctaa-atttataggctaataatattca--gtcgttttttaagatcagattac---tcttttacgttgcagGTTAAATGTTTGATGCGTCAGTTGATATCTGGTTTGGAGCATTGTCATAGTCGTGGTGTACTTCATCGTGACATCAAAGGATCAAATCTTCTTATTGATG
           ||   | ||| ||| |    |    |||||  | || |||  | |   ||||||  ||   |  || | ||    | |  | ||   | ||| |  ||  |||| |||||||  |||   ||  |  |||||||  | ||||||||||| |  || ||||| ||||| ||||||||||||||||||||||| ||| ||||| 
gttagactgaattgtcttggcatttgaaacaaatatgcattggcaaacattctttgcaaaataatgatcgtggatgtatgttgcctttatttaacatatgtttcatattatagGTCAAATGTTACATGAAACAACTACTATCTGGCCTAGAGCATTGTCACAACCGCGGTGTGCTTCACCGTGACATCAAAGGATCAAATCTCCTTCTTGATA

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|125258415|gb|EL272500.1|EL272500
EST:     TTTGGCTGGTCTTGCTTCAAGTCCTGTTGTTAAGTTCTCAGAATCAGAAG                         GTTAAATGTTTGATGCGTCAGTTG
genomic: TTTGGCTGGTCTTGCTTCAAGTCCTGTTGTTAAGTTCTCAGAATCAGA-Ggttagttagg ... tacgttgcagGTTAAATGTTTGATGCGTCAGTTG
EST: gi|116455375|gb|EG497967.1|EG497967
EST:     ATTTGGCTGGTCTTGCTTCAAGTCCTGTTGTTAAGTTCTCAGAATCAGAG                         GTTAAATGTTTGATGCGTCAGTTGATATCTGGTTTGGAGCATTGTCATAGT
genomic: ATTTGGCTGGTCTTGCTTCAAGTCCTGTTGTTAAGTTCTCAGAATCAGAGgttagttagg ... tacgttgcagGTTAAATGTTTGATGCGTCAGTTGATATCTGGTTTGGAGCATTGTCATAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggctaataatattcagtcgttttttaagatcagattactcttttacgttgcagGTTAAATGTTTGATGCGTCAGTTGATATCTGGTTTGGAGCATTGTCATAGTCGTGGTGTACTTCATCGTGACATCAAAGGATCAAATCTTCTTATTGATG
  ggctaat  putative branch site (score: 3)
                                    ttactctttt  putative PPT
     taataatattcagt  TA-rich tract