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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgcagctaacatgtttgataaattcatcttgcaatttctaatcagatatcaatatctcatcttttatcttgttattgtag

Basic information

species Arabidopsis thaliana
transcript AT5G50850.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA14G36540.2 (Glycine max), 5'ss of exon 4
ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgcagctaacatgtttgataaattcatcttgcaatt--tctaatcagat-atcaatatctcatcttt--tatcttgttattgtag-----------------------
        ||| |||||||| || || ||| | |||||||||||||| |||||||||||||| ||  | ||||||||||||||| |        |   ||  |   |  ||  |     | ||  | || |    |   |||  |||| | ||    |  |  ||    ||                        
--------CAGGGATGCTCTCAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTCTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttagttagttagtttagttgtcttgccaacctctccttttaagaacttcattgacttaactttcttccttctttcattttag

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA14G02380.2 (Glycine max), 5'ss of exon 4
ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgtt----agttgcagctaacatgtttgataaattcatcttgcaatt--tctaatcagat-atcaatatctcatctttt--atcttgttattgtag-------------------
        ||| || ||||| || || ||| | |||||||||||||| |||||||||||||| ||  | |||||||||||||||    | |  |||    |||    | |   ||  |       ||  | || |    |   |||  |||| | ||    |  |  |||   ||                    
--------CAGGGAGGCTCTGAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttggttggttggttggtttagttgtcttgccaacctctccttttaagaacttcattaacttaactttcttctttcattttag

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 4
ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttag----ttgcagctaacatgtttgataaattcatcttgcaatttctaatcagatatcaatatctcatctttt-----atcttgttattgtag------------
        ||| || ||||| || || ||| | |||||||||||||| |||||||||||||| ||  | ||||||||||||||| |    |  |||    |||    | |   ||  |     | || ||   |   | |    | |   || | |     |  |  |||   ||             
--------CAGGGAGGCTCTGAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgcttccttagttgctttacttgtcttgccaccctctcctcttaagaacttcattaacttaactttcattttag

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 5'ss of exon 4
ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgcagctaacatgtttgataaattcatcttg-----caatttctaatcagatatcaat-atctcatcttttatcttgttattgtag-------
|||||||| || ||||||||||| |||||| |||||||||||||||| || ||||||||||| ||| | |||||||||||||| ||    ||   | | |  ||      |   |||      || ||  |  ||   | ||| |  ||     | |||| || | ||| | |       
ATGACAGTGAGGGATGCTCTAAACTCTGCACTTGATGAGGAAATGTCCGCAGATCCTAAAGTCTTTTTGATGGGTGAAGAGgtgaggaaaagtggataggaatgcctcccttggctttgttctcacttgtttctcctttttcatttgtccttgttcttatgttctgatttttgtttacag

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ19158 (Selaginella moellendorffii), 5'ss of exon 1
ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgcagctaacatgtttgataaattcatcttgcaatttctaatcagatatcaatatctcatcttttatcttgttattgtag
||||| ||  | ||||| || || || || ||||| ||||| ||| |||| ||||||||||| ||||| ||||| ||||||||  | |    |    |   | |||   ||  |||| | ||| ||     |  || ||| | ||                      
ATGACTGTTCGTGATGCGCTCAACTCCGCCATTGACGAGGAGATGGCTGCCGATCCTAAAGTGTTTGTGATGGGAGAAGAGgtatgctttctccttta---tcgatgcttttttctttccattccttgatgggaatgaatgtgtccag-------------------

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ13549 (Selaginella moellendorffii), 5'ss of exon 2
ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgcagctaacatgtttgataaattcatcttgcaatttctaatcagatatcaatatctcatcttttatcttgttattgtag
||||| ||  | ||||| || || || || ||||| ||||| ||| |||| ||||||||||| ||||| ||||| ||||||||  | |    |    |   | |||   ||  |||| | ||| ||     |  || ||| | ||                      
ATGACTGTTCGTGATGCGCTCAACTCCGCCATTGACGAGGAGATGGCTGCCGATCCTAAAGTGTTTGTGATGGGAGAAGAGgtatgctttctccttta---tcgatgc-tttttctttccattccttgatgggaatgaatgtgtccag-------------------

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|124712593|gb|EH803995.1|EH803995
EST:     TTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG                         GTTGGCCAATATCAAGGTGCC
genomic: TTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgca ... gttattgtagGTTGGCCAATATCAAGGTGCC
EST: gi|164016936|gb|ES123772.1|ES123772
EST:     TGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG                         GTTGGCCAATATCAAGGTGCCTACAAG
genomic: TGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgca ... gttattgtagGTTGGCCAATATCAAGGTGCCTACAAG
EST: gi|164137578|gb|EL978552.1|EL978552
EST:     TCATGGGTGAAGAG                         GTTGGCCAATATCAAGGTGCCTACAAG
genomic: TCATGGGTGAAGAGgttagttgca ... gttattgtagGTTGGCCAATATCAAGGTGCCTACAAG
EST: gi|116443796|gb|EG486388.1|EG486388
EST:     TTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG                         GTTGGCCAATATCAAGGTGCCTACAAG
genomic: TTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgca ... gttattgtagGTTGGCCAATATCAAGGTGCCTACAAG
EST: gi|116376958|gb|EG419550.1|EG419550
EST:     TTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG                         GTTGGCCAATATCAAGGTGCCTACAAG
genomic: TTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgca ... gttattgtagGTTGGCCAATATCAAGGTGCCTACAAG
EST: gi|125265385|gb|EL279470.1|EL279470
EST:     TGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAG                         GTTGGCCAATATCAAGGTGCCTACAAG
genomic: TGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgca ... gttattgtagGTTGGCCAATATCAAGGTGCCTACAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttagttgcagctaacatgtttgataaattcatcttgcaatttctaatcagatatcaatatctcatcttttatcttgttattgtag

- - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA