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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatgacttactcgacttggcggacccctccagtgttactttcctctctaactattcaagtaatttaaatgctggtttattcag

Basic information

species Arabidopsis thaliana
transcript AT1G10950.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 5'ss of exon 9
GAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatgacttactcgacttgg-----cggacccctccagtgttactttcctctctaactattcaagtaatttaaatgctggtttattcag-----------
| ||||  | ||| ||||||| ||||| |||||||||||||| || |||||| | ||||| ||||| || |||||  | |||||||| |  || ||||||  |   ||   ||||     |       ||  || ||| ||  || |  || |       |  |  |  | ||| || ||               
GCGAGGGTCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGCTATGTCAGTGGTGGCCTCTACTCAAGGAATGGTGgtatggttctttccttttggaattgcattattttcttgtattatttgtctgtgcaattcaatctcttctcaaggttctgtttcatagtttcctcctgtca

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G026231_T01 (Zea mays), 5'ss of exon 9
GAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatgacttactcgacttggcggacccctccagtgttactttcctctctaactattcaagtaattta-aatgctggtttattcag-----------------------------------------------------------------------------------------------------------------
| |||| || ||| ||||||| ||||| |||||||||||||| || || ||| | ||||| ||||| || |||||  | |||||||| ||||| ||||||  |       || | |      ||  | | ||  | |    |    | |||||  |  |||  |||     |||  |                                                                                                                    
GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCGTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAGCGGTGgtatggtt-------ctggacacttttctttaattttcatgtttgtttgcgcaattcagtttctttgcaatatctctttccttgacgtaccttcatgttcttctatttcaaaaatagtctgcagtttaacttgtcatgtatggaatcctcacctcacaatctatatggcttaccgattgcttcttgaattcatggcag

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 9
GAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatgact-tactcgacttggcggacccctccagtgttactttcctctctaactattcaagtaatttaaatgctggtttattcag---------------
| |||| || ||| ||||||| ||||| |||||||||||||| || |||||| | ||||| ||||| || |||||  | |||||||| |  || ||||||  | | | | | ||            ||   ||  || |     | | | |    | ||| |   |     | || ||                 
GCGAGGGGCTATCATCACAACCTTCATTGTGTGCTATGCTCTTACATCTTTTATTTCTGGATATGTTAGTGGTGGTCTTTACTCAAGGAATGGTGgtatggttctgcacaattttctattaattctcatgtttgtttgcacaattcagtttctttgcaatctctgtttccatatagtcccttcatggtcttctcc

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA08G13370.1 (Glycine max), 5'ss of exon 9
GAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatga--cttactcgacttggcgga----cccctccagtgt-------tactttcctctctaactattcaagt--aatttaaatgctggtttattcag------------------
| ||||||| ||| |||| |||||||| ||||| |||||||| || |||||| | |||||||||||||| || || ||||||||| |||  ||||||| ||  |||  |  | ||   | |    | |  | ||| |       |   ||  ||||   ||  ||   |    ||| |||| |  | ||   |                   
GCGAGGAGCCATCATCACTACTTTCATTGTGTGTTATGCTCTCACATCTTTTATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGAAATGGGGgtaagaatcttctttaattttctgtattttcgctcctagtatgtttgggtggctttgtctcagtcttctccttttggttttgaatgattatgtaactattttttatctgtttgttag

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 9
GAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatga-cttactcgacttggcggacccctccagtgttactttcctctctaactattcaagtaatttaaatgctggtt----tattcag
  ||||||| || |||||||| ||||| || ||||||||||| || |||||  | |||||||||||||| || |||||||||||| | |  ||||||| ||  || |     |    |   |      || ||   | | |||||  |  |   | | |||  ||   || ||    | |||||
ACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGGgtaagaatttgcattgatctttgctacatgtttgt-ttgggtgcttctctctccctctgaatgattataaccgtgcttataattttcag

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA05G30210.1 (Glycine max), 5'ss of exon 9
GAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgta--tgacttactcgacttggcgga----cccctccagtgt-------tactttcctctctaactattcaagtaa--tttaaatgctggtttattcag----------------
| ||||||| || ||||| |||||||| ||||| |||||||| || |||||  | |||||||||||||| || || ||||||||| |||  |||||||  |  |||  |  | ||   | |    | |  | ||| |       |   ||  ||||   ||  ||   |    ||| |||| |  |  |   |                 
GCGAGGAGCCATTGTCACTACTTTCATTGTGTGTTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGAAATGGGGgtaagtatcttctttaattttctgtatattcgctccaagtatgtttgggtggctttgtctcagtcttctctttttggttttgaatgattatgcaactaatttttatgtttgttag

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 9
GAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatgacttac-tcgacttg----gcggacccctccagtgttacttt---------------cctctctaactattcaagtaatttaaatgctggtt----tattcag
  ||||||| || |||||||| ||||| || ||||||||||| || |||||  | |||||||||||||| || || ||||||||| | |  ||||||| || |  | | ||  |      |     |      ||||  |||                ||||||  || |   | | |||   |   || ||    | |||||
ACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGTAATGGGGgtaagattcgcattgatctatgctacatgttctcttgatgtttgtttaggtgcctctctctctctctctctctctctgaatgattatgactgtgcttatcattttcag

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 5'ss of exon 9
GAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgta--tgacttactcgacttggcggacccctcc-agtgttactttcctctctaactattcaagtaatttaaatgctggtttattcag--------------------------------------------------------------------------------------------------
|||||||||||| ||||| ||||| |||||||| |||||||| || || ||  | || ||||||||||| ||||||||||||||  | |  || ||||  | | ||   |    ||  |   | |||  ||| ||   |  | | |||| | |||| |||    |      |  |  ||  |                                                                                                  
GAGAGGAGCAATTGTCACGACTTTTATAGTGTGTTATGCTCTTACATCATTCATTTCGGGTTATGTGAGTGGTGGAATGTACTCCCGCAATGGTGgtaagtaatttgtacattatgttgcctcactcttagtcttctgtcaccccctaaat-ttcatgtacgaaaggcatggcctgtttttgattcttttattgtcaatgaatctcttctataaatggtcatttcctctgtcttatcagcatttgtttactggtggcttattactgtgtctacttgtcag

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 9
GAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatg-acttactcgacttggcggacccctccagtgttactttcctctctaactattcaagtaatttaaatgctggtttattcag------------------------------------------------------------------------------------------------
|||||||||||| ||||||||||| ||||| || ||||||||||| || ||  | || ||||||||||| ||||| ||||||||| | |  || |||||| ||||  ||        || |     |   ||| |||   | |||     |||     || |   |  || ||| ||  |                                                                                                
GAGAGGAGCAATTGTCACAACTTTTATAGTATGTTATGCTCTGACATCATTCATTTCGGGTTATGTGAGTGGTGGGATGTACTCACGCAATGGTGgtatgtacttcatccgtcaactggtcgatggctaagtttcttgtttttctgggc-ttccttccatatcttttgtgctttttttgggttatatttaacaagtatttcttgatatgttctactcaactgtctttgtgattgcttctggtgctaaattatatcacttctctgtcatcttgtcag

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|164197654|gb|ES142568.1|ES142568
EST:     TTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGG                         GTAAACATTGGATCAAGTGCATGGTCC
genomic: TTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatgactta ... gtttattcagGTAAACATTGGATCAAGTGCATGGTCC
EST: gi|125284758|gb|EL298843.1|EL298843
EST:     TTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGG                         -TAAACATTGGATCAAGTGCATGGTCCTCACGGCTTCT
genomic: TTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatgactta ... gtttattcagGTAAACATTGGATCAAGTGCATGGTCCTCACGGCTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAGGAGCAATCGTCACAACTTTCATAGTGTGCTATGCTCTGACTTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatgacttactcgacttggcggacccctccagtgttactttcctctctaactattcaagtaatttaaatgctggtttattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC