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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaaaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA

Basic information

species Arabidopsis thaliana
transcript AT3G25800.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 7
acaaaaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
     || |      | |   |    | | |  |      |||         | ||   || |    |   | |   |  |  | ||   | | ||  |||| || ||  |||| || || ||||| || ||||||||| |  |||| ||||||||||| ||||| ||  | |||||||| ||||||||||| ||||| |
ttgttaacgtacaacaatactgctaatctttattggtacttgtcaacagctaaatgctgatctaattgtactgactgttccagttttgacttttttgcagGACGCCACTCTTGAACAACTGCTTCCCATTTTTCTTTCTTTGCTGAAGGATGAGTTCCCTGATGTTCGACTCAACATTATAAGCAAACTTGATCAAGTTA

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
------acaa--aaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
      | ||  ||   | | || ||     ||  || |||||   |  |||||  ||||  |||  ||||     || | |  |  || || | ||    |||  |||| |||||||||||||| || ||||| || || ||||| || ||||| ||||| || || || |||||| | |||||||||||||| ||||| |||||||
taaaagataatcaacaaaatctattttctaggctattgttatagtagtagttttatttgg--tgtaaatgt---gcatctcagttctaccttatcttc---attgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 7
acaaaaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgtt---gttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
| ||||   |||  |    |  |   |||  ||  |    |||  | |  | | | | | || || | || | ||  |||  |     || | |  |||  |||| |||||||||||||| || ||||| || || ||||| || ||||| ||||| || || || || ||| | |||||||||||||| ||||| |||||||
ataaaagatagtaca--caaaatctattttctaggctaattgtgatagcagtagttttt-tggtgtaaatgtgaatctcagttctaccttatcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGA

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 7
-acaaaaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
   ||   |     |||| |  |||      || |  |   | ||||  ||  |   | |       |   |     || | ||  |||| | ||||  ||||||||||||||||||| || ||||| || ||||| || || ||||| ||||| || || ||||||||| | || || || ||||| ||||| |||||||
tttaatgctacaactaat-gctgtggcagcattgtttaacctttttttctttcaaaatttccaagaaactatgcctgtttatgtgtttttctttattgcagGATGCAACAATTGAGCAGCTTCTTCCTATTTTTCTCTCCCTTTTGAAGGATGAATTTCCTGATGTACGCCTAAATATCATAAGCAAGCTTGATCAAGTGA

upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 6
acaaaaatgagttta--attgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgca---gattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
    || |||  | |  ||| |  |   ||     | ||   | || || |  |||  ||| | ||| |   |||||         ||  |  || ||  |  |||||||||||||||| || || |||||||| ||||||||||| ||||| ||||| || || ||||||||  | || || || ||||| ||||| ||| | |
---caattgatctcacaattcaaatttattgggagtgcat--ttttctgttaagatcatgtttcttgaattggatttctgaactttgtcttggttgctgatgcagGATGCAACAATTGATCAACTTCTTCCAATTTTTCTTTCTCTTTTGAAGGATGACTTTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAA

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|125014859|gb|EL087128.1|EL087128
EST:     ATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG                         GATGCAACAATTGAGCATCTCCTTCCAATCTT
genomic: ATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAGgtaagagagt ... tctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTT
EST: gi|164131740|gb|EL975680.1|EL975680
EST:     GATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG                         GATGCAACAATTG
genomic: GATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAGgtaagagagt ... tctattttagGATGCAACAATTG
EST: gi|86040356|gb|DR336111.1|DR336111
EST:     GATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG                         GATGCAACAATTGAGGCATCTCCTTCCAATCTTTCTTTCTCTATTTGAAAG
genomic: GATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAGgtaagagagt ... tctattttagGATGCAACAATTGAG-CATCTCCTTCCAATCTTTCTTTCTCTATT-GAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA
                        ttttaac  putative branch site (score: 2)
                                     ttgttttttctatttt  putative PPT
                                     ttgttttttctatttt  TA-rich tract