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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagactatcctatcagtagagttgtattgtcatttgcatctcgttttgttggtttttctgagtttgtctatttcgtttgatgttttttgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTATTTAATGGGCGGAGGAATGATGGGGGGCAAGCTGAGTATACCTGCCCAT

Basic information

species Arabidopsis thaliana
transcript AT1G16710.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 7
gtaaga--ctatcctatcagtagagttgtattgtcatttgcatctcgttttg-----ttggtttttctgagtttgtctatttcgtttgatgttttttgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTATTTAATGGGCGGAGGAATGATGGGGGGCAAGCTGAGTATACCTGCCCAT
|||||   || |   ||   | | | | |  ||||  |  ||||    ||||      |   |||| |   ||      |||    |||||| || || ||||||| || ||||| || ||| |   ||||||||| || ||||||||||||||||||||  | ||||||||||| |||||||| ||||| ||||||||| 
gtaagttcctttttcatttttggtgattttgtgtctgtatcatcaaaatttgggtatcttccttttgtatattaaatctttttaaatgatgtattctgcagTGGGTTCAGTGTGACAAGTGTGAATGCTGGCAGCACCAGATATGTGCTCTATTTAATGGTAGAAGGAATGATGGAGGGCAAGCAGAGTACACCTGCCCAA

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 6
----gtaagactatcctatcagtagagttgtattgtcatttgcatctcgttttgttggtttttctgagtttgtctatttcgtttgatgttttttgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTATTTAATGGGCGGAGGAATGATGGGGGGCAAGCTGAGTATACCTGCCCAT
    ||    |  | | ||   || |  |  |   |||   |  |||  | || ||     ||  | | |   |  ||||   | |||  || || ||||||| |||||||| ||||||||   |||||| |||||||| |||||||||||||||||  | ||||| | ||| || |||||||| ||||| |||||  
gtatgttttgcagttccattgatacacataaaagctcaaaagtttctaatattttt----ctttggtgctaaacattttcaaatcatgcattctgcagTGGGTTCAATGTGACAAATGTCAATGCTGGCAACATCAAATTTGTGCTCTATTTAATGGAAGAAGGAACGGTGGAGGACAAGCTGAATATACTTGCCCCC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
gtaagactatcctatcagtagagttgtat-tgtcatttgcatctcgttttgttggtttttctgagtttgtctatttcgtttgatgttttt-tgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTATTTAATGGGCGGAGGAATGATGGGGGGCAAGCTGAGTATACCTGCCCAT
            | | |   | |   ||| |||||||||    | |||  | |   |||| |   ||| |  |   | | |  | | | | || ||||||| ||||||||||||||| | || ||||| |||||||| |||||| ||||||||||  | || |||||||| || |||||||| ||||| |||||  
---------gtatgttaagtgtgccatatgtgtcatttgg---ttgttcagctaagtttttttgttttattaac--catctattctctgtgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 7
gtaagactatcctatcagtagagttgtattgtcatttgcatctcgttttgttggtttttctgagtttgtctatttcgtttgatgttttttgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTATTTAATGGGCGGAGGAATGATGGGGGGCAAGCTGAGTATACCTGCCCAT
    |  |||| | ||  |    |||| |  | ||| |||  |   ||||||    ||  | |     |||| ||  | ||        || ||||||| ||||||||||||||| |||| ||||| |||||||| |||||  |||||||||| || || |||||||| || |||||||| || || |||||  
--gtgcgtatcatgtc--ttattttgtttattgattggcagtttactttgtt----ttaataa--ccatctactttatctg------catgcagTGGGTTCAATGTGATAAATGTGAGGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTCGAAGAAATGATGGTGGACAAGCTGATTACACTTGCCCTA

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
gtaagactatcctatcagtagagttgtattgtcatttgcatctcgttttgttggtttttctgagtttgtctatttcgtttgatgttt-tttgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTATTTAATGGGCGGAGGAATGATGGGGGGCAAGCTGAGTATACCTGCCCAT
            | | |   | |   | |     ||||    ||  ||     |||||| ||  ||| |  |   | | |  | ||| | || ||||||| ||||||||||| ||| | || ||||| |||||||| |||||  ||||||||||  | || |||||||| || |||||||| ||||| |||||  
---------gtatgttaagtgtgccatgtgtcattttgttgttcagttaacaagtttttttgt-tttattaac--catctattctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 6
gtaagact-atcctatcagtagagt-tgtattgtcat-ttgcatc-tcgttttgttggtttttctga-gtttgtctatttcgtttgatgttttttgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTATTTAATGGGCGGAGGAATGATGGGGGGCAAGCTGAGTATACCTGCCCAT
||| |  | || |  |   |  ||| | | |  | || ||| ||  | || |      |   ||| | |||||   ||||  ||     | ||||| ||||||| |||||||| |||||| | || ||||| |||||||| |||||  | || ||||| |||||||||||||| ||||| ||||| ||||| |||||  
gtatgttttattcatttcttttagtatctgtcattatgttggattattgtctgagcaatcgctcttatgtttgaacatttgcttc----tattttgcagTGGGTTCAATGTGACAAATGTGAAGCTTGGCAACATCAAATTTGTGCCTTGTTCAATGGTCGGAGGAATGATGGTGGGCAGGCTGAATATACTTGCCCTA

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|116434362|gb|EG476954.1|EG476954
EST:     AAAACGATGAAGAGATTGAAGAATCG                         TGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTA
genomic: AAAACGATGAAGAGATTGAAGAATCGgtaagactat ... ttttttgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctcgttttgttggtttttctgagtttgtctatttcgtttgatgttttttgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTATTTAATGGGCGGAGGAATGATGGGGGGCAAGCTGAGTATACCTGCCCAT
                                     gtttgat  putative branch site (score: 5)
                                           tgtttttt  CT-rich tract
                                          atgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagactatcctatcagtagagttgtattgtcatttgcatctcgttttgttggtttttctgagtttgtctatttcgtttgatgttttttgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTATTTAATGGGCGGAGGAATGATGGGGGGCAAGCTGAGTATACCTGCCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA