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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaatatatgatttgctggtatcaattcatttctgacgctgaggcactgcttatgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT

Basic information

species Arabidopsis thaliana
transcript AT1G71220.1
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 30
lower sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 33
gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaat--atatgatttgctggtatcaattcatttctgacgctgaggcactgctta---tgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
     |      | |||   | ||   |    |     ||  |  |  || | | |||     |  ||| || |  | ||  || |   ||  | |   || |||||| || || ||  | |||||||||||||| ||||| || ||||| ||  |||||||||| ||||||||||| || ||||| || ||||||||||  |||
-----tggattctataatattttttcatatttagttggagcctggtggattttacttgtcatcaggaatgcaatcttcactttgtgcttcttgtcaatttgccagATATGAACGCTTTATGAAGATTATGATTCTAAGTGTTCTAAAGAATACTCATCGTCCTGTTAAATTCTGGTTCATAAAGAACTACCTCTCTCCTCCTTTT

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 30
lower sequence: GLYMA05G30230.1 (Glycine max), 3'ss of exon 31
---gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaatatatgatttgctggtatcaattcatttctgacgctgaggcactgctta---tgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
    |  |||| | ||||   | | |  |  || |          |  ||| | |||||     |   || || |  | ||  || |   ||  | |   || |||||| || || ||  | |||||||||||||| ||||| || ||||| ||  ||||||| || ||||||||||| || ||||| || ||||||||||  |||
ggattctataatattttttcatatttagttggagcctgg------tggtattttatttgtaatcagggatgcaatcttcactatgtgcttcttgtcaatttgccagATATGAACGCTTTATGAAGATTATGATTCTAAGTGTTCTAAAGAATACTCATCGTCCAGTTAAATTCTGGTTCATAAAGAACTACCTCTCTCCTCCTTTT

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 30
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 31
gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaatatatgatttgctggtatcaattcattt-ctgacgctgag-gcactgcttatgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
 |   ||   |     ||| |    |     |     | ||||  | | |  | |  |   |  ||||  | | || |   | |  |   |||||    |||||| || ||||| || || || |||||||| |||||||||||||||| |||||| || ||||||||||||||||| ||||| ||||| ||||||||||||
-tttctacagggagggagtctgcgctaattcctgtttatgttttgtttgtt-tgtagtaccagaaattgctctgctaatatttaatggtttgctttctgcagATATGAACGTTTTCTGAAAATCATGATTCTAAGTGTCCTGAAGAACAGCAATCGCCCCGTAAAATTCTGGTTTATAAAGAACTATCTTTCTCCTCAATTT

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 30
lower sequence: EFJ07070 (Selaginella moellendorffii), 3'ss of exon 27
gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaatatatgatttgctggtatcaattcatttctgacgctgaggcactgcttatgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
                                          |||  | | |  || | | ||  || |   | |  | | || |   |||       |||||||||||||| || ||||||||||| ||||| ||  ||||||| || |  || || || ||||| |||||||| ||||||||||| ||||| ||||||
-----------------------------------------gtaa-gtcttagatgtttgaat-gatccgactttctcacagaaggtttgc-------agATACGAGCGTTTTCTAAAGATTATGATGCTCAGCGTTTTGAAGAATACTAGACGGCCAGTGAAATTTTGGTTTATCAAGAATTATCTTTCTCCACAATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgatttgctggtatcaattcatttctgacgctgaggcactgcttatgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
                          ttctgac  putative branch site (score: 2)
                   aattcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaatatatgatttgctggtatcaattcatttctgacgctgaggcactgcttatgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - -caaaaaa