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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattccgtttctttatttttacaaaatttctttgtgagttgagtttgtggtttaacggtgtttttattttccagGCTGCTCGTGCTTTAGCTAATTTGGCTGCTCATGGAGATAGCAACAATAATAATGCTGCGGTTGGGCAAGAAGCAGGTGCATTAGAAGCTCTTGTCCAAC

Basic information

species Arabidopsis thaliana
transcript AT2G44900.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44900.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os10g41360.1 (Oryza sativa), 3'ss of exon 4
-----------------gtaa-attccgtttctt-tatttttacaaaatttctttgtgagttgagtttgtggtttaacggtgtttttattttcca----gGCTGCTCGTGCTTTAGCTAATTTGGCTGCTCATGGAGATAGCAACAATAATAATGCTGCGGTTGGGCAAGAAGCAGGTGCATTAGAAGCTCTTGTCCAAC
                  ||    |  || | ||  ||  | ||||    | | | ||   ||  |||    | |||   | |   | || | ||    ||||||  | || |||||||| || || || |||||||||| ||||||||||||||| || || || || |||||||| ||  | || ||  | || || |
tccatctaacttgctacctagtgctttgtcttttacatgctcacaatcactgtatatgtactgcatttactttctaatactatcactgttgttcatgtagGCTGCAAGGGCATTAGCTAACTTAGCCGCACATGGAGATAACAACAATAATAATGCCGCTGTGGGTCAGGAAGCAGGGGCTCTTGAGGCATTAGTGCAGC

upper sequence: AT2G44900.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G48840.1 (Glycine max), 3'ss of exon 4
-------------gtaaattccgtt---tctttatttttaca---aaatttctttgtgagttgagtttgtg-gtttaacgg---tgtttttattttccagGCTGCTCGTGCTTTAGCTAATTTGGCTGCTCATGGAGATAGCAACAATAATAATGCTGCGGTTGGGCAAGAAGCAGGTGCATTAGAAGCTCTTGTCCAAC
             |||  ||   |    ||||    | | ||   |    | |  |||| |||   | |   | |||||     |  | |||  |  |||||||||||||| || ||||| || ||||| ||||||||||| |||| ||| ||||| || ||||| ||||||||||||||  | || ||||| || ||||
tgattcttcagttgtatgttttttcaaatcttgtcctctccattgagggatgtaagtgaattggtctaggatgattaacataactactgttaaatatcagGCTGCTCGTGCATTGGCTAACTTAGCTGCCCATGGAGATAGTAACAGTAACAATGCCGCTGTTGGACAAGAAGCAGGTGCTCTTGATGCTCTCGTTCAAC

upper sequence: AT2G44900.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 5
----------------------gtaaattccgtttctttatttttacaaaatttctttgtgagttga-gtttgtggtttaacgg---tgtttttattttccagGCTGCTCGTGCTTTAGCTAATTTGGCTGCTCATGGAGATAGCAACAATAATAATGCTGCGGTTGGGCAAGAAGCAGGTGCATTAGAAGCTCTTGTCCAAC
                       |||| ||   | || |   || |   |   |     ||| |||  ||  |  | |||||     |   ||||     ||||||||||| || || ||||| || ||||| ||||||||||| |||| ||| |||||||| ||||| ||||||||||||||  | || |||||||| ||||
tgattcttcagttgtatgttttttaaaatcttgtcctctccattgaggga---tgcacatgaattggtgtgggatgattaacataactacctttaaacatcagGCTGCTCGGGCATTGGCTAACTTAGCTGCCCATGGAGATAGTAACAGTAACAATGCTGCCGTTGGACAAGAAGCAGGTGCCCTTGAGGCTCTTGTTCAAC

upper sequence: AT2G44900.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv15s0021g01810.t01 (Vitis vinifera), 3'ss of exon 5
------------gtaaat-tccgtttctttatttttacaaaatttctttgtgagttga---gtttgtggtttaacg--gtgtttt-----tattttccagGCTGCTCGTGCTTTAGCTAATTTGGCTGCTCATGGAGATAGCAACAATAATAATGCTGCGGTTGGGCAAGAAGCAGGTGCATTAGAAGCTCTTGTCCAAC
            | | || |  || | |  |||   ||| | | | | | |||  |||   |||  |  || |  |  |||  ||     ||  | ||||||||| ||||| || |||||||||||||||||||||||||||||||  || |||||||| ||||| ||||| ||||||||| | ||||| ||||| | ||
cagcttgcatttgcacatgtttgtgtttacattagcacatattgtatatatgaagtgatctgttgctaattaattgtcgtgacttctgagtacataccagGCTGCACGTGCCTTGGCTAATTTGGCTGCTCATGGAGATAGCAACAGCAACAATGCTGCTGTTGGACAAGAGGCAGGTGCACTTGAAGCACTTGTGCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaaaatttctttgtgagttgagtttgtggtttaacggtgtttttattttccagGCTGCTCGTGCTTTAGCTAATTTGGCTGCTCATGGAGATAGCAACAATAATAATGCTGCGGTTGGGCAAGAAGCAGGTGCATTAGAAGCTCTTGTCCAAC
                              gtttaac  putative branch site (score: 3)
                                       tgtttttattttcc  putative PPT
                                       tgtttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattccgtttctttatttttacaaaatttctttgtgagttgagtttgtggtttaacggtgtttttattttccagGCTGCTCGTGCTTTAGCTAATTTGGCTGCTCATGGAGATAGCAACAATAATAATGCTGCGGTTGGGCAAGAAGCAGGTGCATTAGAAGCTCTTGTCCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC