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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgccttagaatctcaattgtatgttgagtataactttctgctgtgtccttattgctgtttccctcactttactgcagCTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCTGGAGAGAACTATTTCTTCACTGCAGGGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G51590.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 11
------------------------gtgccttagaatctcaattgtatgttgagtataactttctgctgtg-tccttattgctgtttccctcactttactgcagCTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCTGGAGAGAACTATTTCTTCACTGCAGGGCAG
                        |||| |  | || |  ||| |     ||   | |  || ||  ||  ||  |   | | |   ||| |||||   ||||||||| ||||| ||||||||||| |||||||| || ||||| ||| | ||||||||||||||||||||   | | ||||||
atctcactgctcattccttctccagtgcatgtggatatttattttgcaacgatattgatattatgaggtaatcactgaagatatgcaccttacttt---gcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGAGAGAACTATTTCTTTCATTCTGGGCAG

upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 10
------------------------gtgccttagaatctcaattgtatgttgagtataactttctgctgtg-tccttattgctgtttccctcactttactgcagCTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCTGGAGAGAACTATTTCTTCACTGCAGGGCAG
                        |||| |  | || |  || ||    |||   | |  || ||  ||  ||  |   | | | | |||  ||||   ||||||||| ||||| ||||||||||| |||||||| || ||||| ||| | ||||| ||||||||||||||   | | ||||||
atcacactgtgcattccttctccagtgcatgtggatatttatggtgcaatgatattgatattatgaggtaatcactgaagatatgtacctttcttt---gcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG

upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G06600.1 (Glycine max), 3'ss of exon 11
----------------------gtgccttagaatctcaattgtatgttgagtataactttctgctgtgtccttattgctgtttccctcactttactg--cagCTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCTGGAGAGAACTATTTCTTCACTGCAGGGCAG
                       ||   |||||    | | || |    | |   | |||    |    |  || |    |      ||   || ||  |||||||| ||||||||||| || || |||||||  |||||||| ||| | || ||||||||||||| |||       || |||
ggtttggatgataattaataatttgtgctagaaatatattggttt--caattgctatttttctttcaaactatactaaattccaatgcatcctattgttcagCTTGCATGGACTTGTTACAATTTCTACCAATTAACACCAACTAAATTGGCAGGAGAGAACTATTACTTTCGCAATGGACAG

upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 6
-------------gtgccttagaatctcaattgtatgttgagtata-----actttctgctgtgtccttattgctgtttccctcactttact----gcagCTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCTGGAGAGAACTATTTCTTCACTGCAGGGCAG
                || |    | ||  ||   | |  || ||       ||||       || | |||   ||  |  ||     || |    ||||||||||||||| || ||||| || ||||| || |||||||| ||| | |||||||||||||||||||||    | ||||||
tgattccttctgccctccctgagttttctcttacttttccagcatttggatgcttttcatgtggttcctatgagtgaattgcttggcctattttttgcagCTTGCCTGGACATGCTATAATTTCTACCAGTCAACACCAACAAAATTGGCTGGAGAGAACTATTTCTTCCACTCTGGGCAG

upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 11
-------------gtgccttagaatctcaattgtatgttgagtata-----actttctgctgtgtccttattgctgtttccctcac----tttactgcagCTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCTGGAGAGAACTATTTCTTCACTGCAGGGCAG
                || |    | ||  ||   | |  |  ||       ||||       || | |||   ||  |  ||       |||  |||||||||||||||| || ||||| || ||||| || |||||||| ||| | |||||||||||||||||||||    | ||||||
tgattccttctgccctccctgagttttctcttacttttccaacatttggatgcttttcatgtggttcctatgagtgaattgcttgggatattttttgcagCTTGCCTGGACATGCTATAATTTCTACCAGTCAACACCAACAAAATTGGCTGGAGAGAACTATTTCTTCCACTCTGGGCAG

upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 11
--------------gtgccttagaatctcaattgtatgttgagta--taactttctgctgtgtccttattgct----gtttccctcacttt--actgcagCTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCTGGAGAGAACTATTTCTTCACTGCAGGGCAG
               |    ||   |  || |||    | |  ||  ||    | || ||| || |  |||       | | | |  | ||  | || ||||||| ||||| ||||||||||| |||||||| ||||| | |||||| ||||||||||||||||| ||  |||| || |||
gtttcttataaaaaatattatactttaccagttgctcatggcttagatagtgctttgttgtctcttgtttgactagaatcttctttgccttctaatgtagCTTGCATGGACATGTTATAACTTCTACCAATCAACACCTATGAAACTGGCTGGAGAGAACTATTTTTTTTCTGCTGGACAG

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|125118997|gb|EL167435.1|EL167435
EST:     TTCACTTGCTGGAGAG                         CTTGCCTGGACTTGTTATAACTTTTTACCAATCGACACCAACGAAACTTGC
genomic: TTCACTTGCTGGAGAGgtgccttaga ... tttactgcagCTTGCCTGGACTTGTTATAAC-TTTTACCAATCGACACCAACGAAACTTGC
EST: gi|116428419|gb|EG471011.1|EG471011
EST:     CAGGTTATGGCCCTGATGAAGNNNNNNNGTTTCTTTCACTTGCTGGAGAG                         CTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCT
genomic: CAGGTTATGGCCCTGATGAAGAAAAAAAGTTTCTTTCACTTGCTGGAGAGgtgccttaga ... tttactgcagCTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgagtataactttctgctgtgtccttattgctgtttccctcactttactgcagCTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCTGGAGAGAACTATTTCTTCACTGCAGGGCAG
                                      ccctcac  putative branch site (score: 3)
                                ctgtttccctcacttt  CT-rich tract
      tataacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgccttagaatctcaattgtatgttgagtataactttctgctgtgtccttattgctgtttccctcactttactgcagCTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCTGGAGAGAACTATTTCTTCACTGCAGGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG