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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctggagcatttgtatcccattttcttgtatacagatttatgatgttctggaattgatcccatttttttgtatacagATGTTGTGAATATGCATTGTTAACACTTGAACATTGGCCTGATGCTCCAGAAATTCAACGATCAGTTGATTTATATGAAGATCTGATTAGATGCTGTGTT

Basic information

species Arabidopsis thaliana
transcript AT2G20190.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 10
gtaagctggagcatttgtatcccattttcttgtatacagatttatgatgttctggaattgatcccatttttttgta----tacagATGTTGTGAATATGCATTGTTAACACTTGAACATTGGCCTGATGCTCCAGAAATTCAACGATCAGTTGATTTATATGAAGATCTGATTAGATGCTGTGTT
          | |  ||| |   | | | ||  | |  |     || | |  ||  | |  |    |||  |||||    | ||| || ||||| |||||| |  | | ||| ||  ||||| |||||||  ||||||| ||||| |||| |||||||||||| ||| |||| | ||||||||| 
----------gtaaatgtgtttgactgtttt-cacattgtccattggtttcttgccagtttttaagtttacttgtactattccagGTGCTGTGAGTATGCACTTCTGATACTGGAGTATTGGGCTGATGCCTCAGAAATACAACGTTCAGCTGATTTATATGAGGATATGATAAAATGCTGTGTC

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 10
gtaagctggagcatttgtatcccattttcttgtatacagatttatgatgttctggaattgatcccatttttttgta-tacagATGTTGTGAATATGCATTGTTAACACTTGAACATTGGCCTGATGCTCCAGAAATTCAACGATCAGTTGATTTATATGAAGATCTGATTAGATGCTGTGTT
|||      | || || |     | |  |  |     ||| || || | ||     | |           |||||| |  || |||||||||||||| |  ||    || ||||||||||||||||| |||||||| || ||||||| |||||||||||| |||||||| |  || ||||||
gtatatatcaacaattattgaaaagtcacaagc---tagagttttggtttttgatcaataccagtggacatttgtactgtagGTGTTGTGAATATGCTTATTTGGTCCTAGAACATTGGCCTGATGCACCAGAAATACATCGATCAGCTGATTTATATGAGGATCTGATAAAGTGTTGTGTT

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G32710.1 (Glycine max), 3'ss of exon 10
gtaagctggagcatttgtatcccattttcttgtatacagatttatga----tgttctggaattgatcccatt---tttttgta-tacagATGTTGTGAATATGCATTGTTAACACTTGAACATTGGCCTGATGCTCCAGAAATTCAACGATCAGTTGATTTATATGAAGATCTGATTAGATGCTGTGTT
          | || | |   | | | |     | ||| |     ||    || | |   ||| || |||||     |||||| |  || |||||||||||||| |  ||    || ||||||||||||||||| || ||||| || ||||||| |||||||||||| |||||||| |  || ||||||
----------gtatatattatcaactattgaaaagacacaagctagagttttggtttttgattaataccattggacatttgtactgtagGTGTTGTGAATATGCTTATTTGGTCCTAGAACATTGGCCTGATGCACCTGAAATACATCGATCAGCTGATTTATATGAGGATCTGATAAAGTGTTGTGTT

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 10
gtaagctggagcatttgtatcccattttcttgtatacagatttatgatg-ttctggaattgatcccat-ttttttgtat-acagATGTTGTGAATATGCATTGTTAACACTTGAACATTGGCCTGATGCTCCAGAAATTCAACGATCAGTTGATTTATATGAAGATCTGATTAGATGCTGTGTT
             | || ||    |  |||||   |  ||| | ||| | || |||  || |    ||    |||||||   || |||||||| |||||  | || | | | |||||||||||||||||  ||||| | |||||||| | |||| ||||||| ||| |||| || |||||||||
------------gtatgaattatctactcttggggatcgatgtgtgagggttttggtttttaattaataccatttgtattgtagGTGTTGTGATTATGCTCTTTTGATATTAGAACATTGGCCTGATGCAGCAGAAGTACAACGATCGGCTGATCTATATGAGGATATGATAAGGTGCTGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtatacagatttatgatgttctggaattgatcccatttttttgtatacagATGTTGTGAATATGCATTGTTAACACTTGAACATTGGCCTGATGCTCCAGAAATTCAACGATCAGTTGATTTATATGAAGATCTGATTAGATGCTGTGTT
                             aattgat  putative branch site (score: 4)
                                   tcccatttttttgt  CT-rich tract
                                       atttttttgtataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctggagcatttgtatcccattttcttgtatacagatttatgatgttctggaattgatcccatttttttgtatacagATGTTGTGAATATGCATTGTTAACACTTGAACATTGGCCTGATGCTCCAGAAATTCAACGATCAGTTGATTTATATGAAGATCTGATTAGATGCTGTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG