Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttcgatattcttctctctctgcatagactttttttcttctcaattctcgtttggttaatggaaacttttcactggattttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG

Basic information

species Arabidopsis thaliana
transcript AT5G62790.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 7
gtttgtttcgatattcttctctctctgcatagactttttttcttctcaattctcgtttggttaatggaaacttttcactggat-tttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG
               |   ||  ||   ||    | | | |  | ||  |   | |  |  |       |  |   |    ||  |    | ||||| ||||| || || | ||| || || || |||||||| || || || ||||||||||||||||| ||||||||||| ||||| || || |||||||| 
--------------gcaagtccatccatatgtgttatatgtact-tcggtaaacatgcgaatcc-----atctcatatcaaatgctcatgacagGGACTGGCCAGTTGACAGGCTGAAAGATGTAAAAGTAGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAAGAAGATCACAGTAGATTCTGCTACT

upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 7
gtttgtttcgatattcttctctctctgcatagactttttttcttctcaattctcgtttggtta-atggaaacttttcac-tggattttga----aaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG
                             |  |    || | |  |  ||   | | |||  | ||  ||||   || | || |  ||||     | ||||| ||||| || || | ||| || || || ||||| || || || || ||||||||||||||||| ||||||| ||| ||||| || || |||||||| 
------------------------gcaagtccatcccttatgtggtatatgtacttctggaaagataaaaacccatctcatgtaaattgatcatgacagGGACTGGCCAGTTGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACT

upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 7
gtttgttt--cgatattcttctctctctgca----tagactttttttc---ttctcaattctcgtttggttaatggaaacttttcactggattttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG
 |||| |    || |  || |  |   |||     |||   | ||| |    |||  ||  ||  || |   ||    |   | | || |||  |  | | |||||||||| || || || || || || |||||||| || ||||| || || ||||| |||||||| ||||| || || || ||||||||||||||||| 
-tttgatcaaggaaaacctgccattgttgctctcttagttctgtttccaggctctatataatcagtttgactataagtatcatccccttgatgattgaca-gGGATTGGCCAGTTGATAAACTGAAAGATGTTAAAGTTGCTGATGCATTAAAACATCCTAACTGGAATATGGGGAAAAAGATAACTGTGGACTCTGCTACC

upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 7
---------gtttgtttcgatattcttctctctctgcatagactttttttcttctcaattctcgtttggttaatggaaacttttcactggattttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG
         |        |  ||| ||       |   |   |||     ||   ||    |  ||||  ||   | | | || |  |||   |||| |  |||||||||| || || || || || || |||||||| || ||||| || || ||||| |||||||| ||||| || || || ||||||||||||||||| 
tttgatcatggaaaacctggcattgttgctctcttagttctgcttccaggctctacataattgatttgactataagtatcattcccttggtgattgaca--gGGATTGGCCAGTTGATAAACTGAAAGATGTTAAAGTTGCTGATGCATTAAAACATCCTAACTGGAATATGGGGAAAAAGATAACTGTGGACTCTGCTACC

upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S62_157V6.4 (Physcomitrella patens), 3'ss of exon 9
------------------gtttgtttcgatattcttctctctctgcatagactttttttcttctcaattctcgtttggttaatggaaacttttca--------ctggattttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG
                   |||  | || |   |       ||     | | |  |     |   |   ||| |    || ||  | | || |||        |  | | | |    |||||||||||||| || ||| | ||||| ||||||||||| ||||| ||||||||||| ||||||| ||||||    ||||| || || || ||||| |||
gtatatgaataagggtatatttcctgcggttgcccaggtggtcacagcaaattcgtggagattgtagaactcatcctctttatccagagttgtcatacatatacgtgttgtcgtttcagGGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAAGCATCCCAACTGGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACG

upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 9
gtttgtttcgatattctt-ctctctctgcatagactttttttc-----ttctcaattctcgtttggttaatggaaacttttcactggatt-ttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG
    |||| |  || | |  | |||   |  |   ||| ||||     ||   ||||    | |||    || ||   ||    || | | |      || |||||||| || || ||| |||| || ||||||||||| ||||| ||||||||||| ||||||| ||||||    ||||| || || || |||||||||
tggagtttaggaatgcgtgttttctgaacgcaacatttgtttcggacatttaaaattaggatatggcagttgtaatagttgatatgcactgtccttttagAGATTGGCCAGTGGAGAAGTTAAAAGATGTTAAAGTAGCAGATGCTTTGAAGCATCCCAACTGGAGCATGGGCCGCAAAATTACGGTTGATTCTGCTACG

upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ09183 (Selaginella moellendorffii), 3'ss of exon 8
gtttgtttcgatattcttctctctctgcatagactttttttcttctcaattctcgtttggttaatggaaacttttcactggattttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG
                         |   || | ||   |         || |   ||    |||  |||||   |      ||   ||  ||||| ||||| || |||| ||| ||||| || |||  ||| |||||| ||||||||||||||||||  |||||||||||||| |||||||| || || || 
------------------------gtaactaaaattgactgaccagtcgttat-acttcaccaatccaaactgaacttctctttaaaaatcagGGACTGGCCAGTGGAAAGGCTCAAGGACGTCAAACCAGCAGATGCGCTGAAGCATCCAAACTGGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACC

upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 8
gtttgtttcgatattcttctctctctgcatagactttttttcttctcaattctcgtttggttaatggaaacttttcactggattttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG
                         |   || | |    |         || |   ||    |||  |||||   |      ||   ||  ||||| ||||| || |||| ||| ||||| || |||  ||| |||||| ||||||||||||||||||  |||||||||||||| |||||||| || || || 
------------------------gtaactaaaatcgactgaccagtcgttat-acttcaccaatccaaactgaacttctctttaaaaatcagGGACTGGCCAGTGGAAAGGCTCAAGGACGTCAAACCAGCAGATGCGCTGAAGCATCCAAACTGGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACC

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|125269961|gb|EL284046.1|EL284046
EST:     ATAATCTTGACTGCATCTGGTGGAGCTTTTAG                         GGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAA
genomic: ATAATCTTGACTGCATCTGGTGGAGCTTTTAGgtttgtttcg ... tttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttctcaattctcgtttggttaatggaaacttttcactggattttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG
                    ggttaat  putative branch site (score: 4)
                                           attttgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttcgatattcttctctctctgcatagactttttttcttctcaattctcgtttggttaatggaaacttttcactggattttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA