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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcgcggaagaactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttgaacatgttatatatgaatag

Basic information

species Arabidopsis thaliana
transcript AT5G49460.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os01g19450.1 (Oryza sativa), 5'ss of exon 9
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcgcggaagaactttcaaagcaatgcctttttt-----ttatctcttgtacaaatc-aaaatagttcttgaacatgttatatatgaatag
||||||  ||||| | ||||| ||  | |||||||| ||||| ||||| ||||| || || || || || |||||||||||||| |||||||| ||||| ||||||   |     |  | ||   || |||  || | ||      ||| |   || |  |||  || || ||  |   |     |           
TGAAGCCCTGAAACAAGGAAAGGTTCAGAAACCTGTTGTTGCATGGGTTAGTGGGACATGCGCTCGTCTATTCAAGTCTGAAGTGCAGTTTGGCCATGCTgtaagtc-tgaaactgttccttttcagtaatttctgtgttgaacagtattttaagtgctcatctgaattaatttattggcccaacag----------

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G179170_T01 (Zea mays), 5'ss of exon 3
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcgcggaagaactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttgaacatgttatatatgaatag---------------------
 ||||| |||||| | ||||| ||  | ||||| || ||||| ||||||||||| || |||||||| || ||||| || ||||| |||||||||||||| ||||||   |   ||  ||||  | | |     ||     ||  |    ||    |||| || | ||  || |  |  |||  ||  ||                       
GGAAGCATTGAAACAAGGAAAGGTTGAGAAACCAGTTGTTGCATGGGTCAGTGGGACATGTGCACGTCTATTCAAATCAGAAGTGCAGTTTGGTCATGCTgtaagttttgaaaaattacttggataccc-caactgcaccttcccctgggtttctatcagaaga-ttggtgtatttactatccatagatctttgtttcttgggatgtaacag

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA07G36840.1 (Glycine max), 5'ss of exon 10
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcgcggaagaactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttga-acatgtta-tatatgaatag-----
 |||||  | ||| | || ||||| | |||||| |||||||||||||| || ||||| ||||||||||||||||| ||||||||||| ||||||||||| ||| ||  |  |    |  |||   |  ||| |    || |    | |   | ||   |    | ||| |||      ||   |  || |||      
GGAAGCCCTAAAACAAGGGAAAGTGACTAAACCAGTGGTTGCTTGGGTTAGCGGAACCTGTGCACGACTCTTCAAATCTGAAGTACAATTTGGTCATGCTgtatgtcactggcccaatatttttgactaattctcagttatagcatttataataagggagccaaattcctgatgttcattggcacttgtataaattag

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA15G15020.1 (Glycine max), 5'ss of exon 9
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggc-gcggaagaactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttga-acatgtta-----tatatgaatag-
 || || || ||| | ||||| ||    ||||| || ||||| ||||||||||| || ||||||||||||||||| ||||||||||| ||||||||||||||| ||  | ||      |  ||  |   ||| |    ||      |     | |||   | |   ||||| |    ||||      |  || |||   
GGAGGCCTTAAAACAAGGAAAGGTATCCAAACCGGTTGTTGCCTGGGTCAGTGGCACATGTGCACGACTCTTCAAATCTGAAGTACAATTTGGTCATGCAgtatgtctcagctcctttaactttgactaaattctcaattaaagcataaaccataaaaggacaacattcttaatgtctgttggctcttgcataaatcag

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA09G04000.1 (Glycine max), 5'ss of exon 9
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggc-gcggaagaactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttga-acatgtta-----tatatgaatag-
 || || || ||| | ||||||||    ||||| || ||||| ||||||||||| || ||||||||||| ||||| ||||||||||| ||||||||||||||| ||  | ||      |  ||  |   ||| |    ||      |     | |||   | |   ||||| |    ||||      |  || |||   
GGAGGCCTTAAAACAAGGAAAAGTATCCAAACCGGTTGTTGCCTGGGTCAGTGGGACATGTGCACGACTATTCAAATCTGAAGTACAATTTGGTCATGCAgtatgtctcagctcctttaactttgacaaaattctcaattaaagcattcatcataaaaggacaacattcttaatgtttgttggctcttgcataaatcag

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA17G03700.1 (Glycine max), 5'ss of exon 8
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagt-ggcgcggaagaactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttgaacat--gttatatatgaatag-----
 |||||  | ||| | || ||||| | |||||| || ||||| ||||| || ||||| ||||||||||||||||| ||||||||||| ||||||||||| ||| ||  | |    |  | |||   |  ||| |    || |    | |   | ||   |    | ||| |||   |  ||   |  || |||      
GGAAGCCCTAAAACAAGGGAAAGTGACTAAACCAGTTGTTGCCTGGGTTAGCGGAACCTGTGCACGACTCTTCAAATCTGAAGTACAATTTGGTCATGCTgtatgtcagtggcccaatatttttttactaattctcagttatagcatttataataagggagccaaattcctgatgttcagtggcacttgtataaattag

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv05s0077g00950.t01 (Vitis vinifera), 5'ss of exon 9
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcg--cggaagaactttcaaagcaa--tgccttttttttatctcttgtacaaatcaaaa-----tagttctt--gaacatgttatatatgaatag------
||||||  ||||| |||||||  | |||||||| || |||||||||||||| |||||||||||||| ||||| || || ||||| || ||||||||||| || ||       |  ||     ||||||   |  ||  |||  | |   || |  || | |  |||     || ||  |   |   || |  | || |          
TGAAGCCCTGAAACAGGGAAAGATTAATAAACCAGTTGTTGCTTGGGTCAGCGGAACTTGTGCACGGCTCTTTAAATCAGAAGTGCAATTTGGTCATGCGgtgagctattacctcaactttattcaaactgaactgtttttgctgtggttccttgactactagaaaggaggtaatttctctaattttgcttgacattatccaactcag

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S46_63V6.3 (Physcomitrella patens), 5'ss of exon 8
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcgcggaagaactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttgaacatgttatatatgaatag--
||| ||||| || ||    || ||||  || || || || |||||||| ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| ||||||  |      || |||   |  || |   | ||  | |||| |||  | | |       | |  ||||  |  ||    ||||||   
TGATGCTTTAAAGGAAAAGAAGGTCAGCAAGCCAGTTGTGGCTTGGGTTAGTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCTgtaagttccttctt-gaccttagtattcattttatcttagtaatctattgatctatttt--cctgatgctgaatttcataagcttgaatacag

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S35_384V6.2 (Physcomitrella patens), 5'ss of exon 8
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcgcggaagaactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttgaacatgttatatatgaatag------------------------
 || ||| |||||||||| || ||   ||| || || || |||||||||||||| || ||||| |||||||||||||| || || |||||||| ||||| ||||||  |     |   |||     |   |      || | |        |    |   |    ||      |   || ||  || |||                         
CGATGCTCTGAAAGAGGGCAAGGTTGGTAAGCCAGTAGTGGCTTGGGTCAGTGGCACATGTGCCCGACTCTTCAAGTCCGAGGTTCAGTTTGGCCATGCTgtaagttccttcacattccttcgtgtgtcttaagcagttgtgaaagtggaaagttgttggagct-ttagccctctccttctacctggatatttacgtcttcgggcttgtctgcag

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ06573 (Selaginella moellendorffii), 5'ss of exon 8
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcgcggaag-aactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttgaacatgttatatatgaatag
||| || |||||  | || ||||| |  |||||||| || || |||||||||||||| |||||   |||||||||||| ||||| || ||||| ||||| |||||||   |   |   | | ||       |  ||   || | || | | |  |                                     
TGAGGCATTGAAGCAAGGCAAAGTGACGAAACCTGTCGTCGCGTGGGTCAGTGGAACCTGTGCCAAACTCTTCAAGTCAGAAGTGCAATTTGGACATGCCgtaagtgcttcaagaccgattctcgtttacgtcactgccttctttcgcgtttgtag------------------------------------

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ31368 (Selaginella moellendorffii), 5'ss of exon 8
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcgcggaa--gaactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttgaacatgttatatatgaatag
||| || |||||  | || ||||| |  |||||||| || || |||||||||||||| |||||   |||||||||||| ||||| || ||||| ||||| |||||||   |   |  ||   | |    |    ||    || | || | | |  |                                     
TGAGGCATTGAAGCAAGGCAAAGTGACGAAACCTGTCGTCGCGTGGGTCAGTGGAACCTGTGCCAAACTCTTCAAGTCAGAAGTGCAATTTGGACATGCCgtaagtgcttcaagaccgattctcctttacgtcaccgccattctttcgcgtttgtag------------------------------------

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ15935 (Selaginella moellendorffii), 5'ss of exon 8
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtg-gcgcggaagaactttcaaagcaatgccttt--tttttatctcttgtacaaatcaaaatagttcttgaacatgttatatatgaatag
 || ||| |  || | |||| |||  | || ||||| || || ||||||||||||||||||||    ||||||||||||||||| |||||||||||||| || |||| |      |  |   | ||  ||| | |||      |  |   || |   |                                    
CGAGGCTCTTCAACAAGGAAGAGTTCACAAGCCTGTTGTCGCGTGGGTCAGTGGAACTTGTGCGAAGCTCTTCAAGTCTGAAGTCCAGTTTGGTCATGCTgtgagtgcggatcttatgatgattaagccaaagtcttagacgctcgttcgttttgtcag-----------------------------------

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ33298 (Selaginella moellendorffii), 5'ss of exon 8
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtg-gcgcggaagaactttcaaagcaatgccttt--tttttatctcttgtacaaatcaaaatagttcttgaacatgttatatatgaatag
 || ||| |  || | |||| |||  | || ||||| || || |||||||| |||||||||||    ||||||||||||||||| |||||||||||||| || |||| |      |  |   | ||  ||| | |||      |  | | || |   |                                    
CGAGGCTCTTCAACAAGGAAGAGTTCACAAGCCTGTTGTCGCGTGGGTCAGCGGAACTTGTGCGAAGCTCTTCAAGTCTGAAGTCCAGTTTGGTCATGCTgtgagtgcggatcttatgatgattaagccaaagtcttagacgctcgtttgttttgtcag-----------------------------------

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|164098096|gb|ES075720.1|ES075720
EST:     GTTTGGTCATGCA                         GGTGCCAAAAGTGGCGGCGAGATGGAGTCTGCACAAGCCAAGAATCAAGCT
genomic: GTTTGGTCATGCAgtaagtggcg ... atatgaatagGGTGCCAAAAGTGGCGGCGAGATGGAGTCTGCACAAGCCAAGAATCAAGCT
EST: gi|86079876|gb|DR375633.1|DR375633
EST:     GTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCA                         GGTGCCAAAAGTGGCGGCGAGATGGAGTCTGCACAAGCCAAGAATCAAGCT
genomic: GTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcg ... atatgaatagGGTGCCAAAAGTGGCGGCGAGATGGAGTCTGCACAAGCCAAGAATCAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcgcggaagaactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttgaacatgttatatatgaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG