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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag

Basic information

species Arabidopsis thaliana
transcript AT1G78900.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 13
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtga-----ttatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag
 ||||| || |  || ||||| |||||||||||||| || || || |||||||| || |||||||||||||| || || ||||| ||||||||||||||||| |      |  | | || ||  |  | |    ||      ||  |   |   ||   | || |      |  ||| | |   |      | | ||  ||                                                                                           
TCCAGATCGGACAGGCAGTGTCACAATTGTTGGTGCTGTCTCTCCACCTGGAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaactgctagattaat-ccaacctttgaattaaattttcaaacctttctaactgcatgttcattgtttgataatcttaactcctctcaattgcag-------------------------------------------------------------------------------------------

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 13
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag
 ||| ||||  ||||||||||||||||||| || || || || || ||||| || || |||||||||||||| || || ||||||||||||||||| ||||| |  |    | | |              |||  |||  |  || |  |  |  |   | |  ||   | | ||||| ||| |  ||  || |||                                                                                           
TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagcagctaa-------------gtctgtcatgattaataatgt--ttat-cgtttcagtgttgttaaaccacatgtt-cttgtttgtag-------------------------------------------------------------------------------------------

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 13
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag
 |||||  | || || ||||| ||||||||||| || || || |||||||| || || |||||||| ||||| || || |||||||| |||||||| ||||| |  |    |   |    | ||||  |||  | ||       |    |  || |   |   |  |||  |  | |   || |||||   | ||            | || |||  |   ||  ||||||| | ||                                                  
TCCAGACAGGAATGGCAGTGTCACAATTGTTGGAGCTGTCTCTCCTCCTGGTGGTGATTTTTCAGACCCTGTTACCTCCGCAACCCTCAGTATTGTTCAGgtaagaaggctgccaaa--ttacttcaatatacttca------gtcctctgatcattagtccagcctgatttacagcgtttgttgtttcaatata---------ttaaatcatatgct---gctctttttttttgcag-------------------------------------------------

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 13
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagt-tttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag
 |||||  | |  || ||||| ||||||||||| || || || ||||| || || || |||||||| ||||| || || |||||||| |||||||| ||||| |      || |      | ||||  ||  |          || |     | ||  ||  || || | |           ||||||  | |||  || |   |   | || | |  |   || |||||                                                          
TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaaga---cggctgccaattacttcaatacttcagtcccccaatcat----tggtccatcctgatttaca-----------gtgtttgttgtttcaatatattgttaaatcatgtgct---gcttttttgcag------------------------------------------------------

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttag-atctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag
 || |||||||  || ||||| |||||||||||||| |||||||| ||||||||||| || ||||| |||||||| || |||||||| || || || ||||| |               ||  |        ||| | | | | | | || |  |||  ||   |   || | |  |||     | ||   || |  |  | ||||| | |      || || |  |                                                             
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaa-------------aactattct------ttcaaatatggttaaaatgg--gtaactgcctgcaaag-taagtcagcctaaggttgtcttgactaattcccgcaaatt-----gttaaaaccct-------------------------------------------------------------

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 14
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaacca-gatggtgtttagttttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag
 || |||||||  || || || || ||||||||||| |||||||| ||||||||||| || |||||||||||||| || |||||||| || || || ||||| |   | |  || |        |    ||     | ||      |  ||        | | |||||  |||| | | |        | |||  |   ||                                                                                       
CCCTGAACGTACAGGTAGCGTAACTATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGATCCTGTGACATCTGCAACCCTGAGCATAGTTCAGgtaaaactatactttaaaatatggttaaaatgggaaactgcctgcaaagtaagtcagcct-taggttgtcatgaccaatgcccacaaattgttaaaagcct---------------------------------------------------------------------------------------

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 14
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttc-atgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag
||||||||||||||| ||||| ||||||||||| || || || |||||||||||||| || || ||||||||||| || ||||| || || ||||| ||||| |  ||    |||  | |     | |  || ||  | ||||| |   ||       ||| |||||   || |   || ||  | || |  |  | |      |||                                                                                 
ACCAGAACGTAACGGTAGTGTCACAATTGTTGGGGCTGTGTCTCCTCCTGGAGGAGATTTCTCTGATCCTGTGACATCTGCAACTCTCAGCATTGTCCAGgtaaagataaaattctgtatgcatcttctaatattaaaatgtagct---attaatacgtatattggt---gaagggtcaaat--ttttaatgtagaaaatgatagcat--------------------------------------------------------------------------------

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 14
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatct-tccattgtagattacat-agtcgtatatgttggttgagatgaac-cagatggtgtttagttttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag
 |||||||| |  || ||||| || ||||| ||||||||||| || || || ||||| ||||||||||| ||||| ||||| || ||||||||||| ||||| ||       ||         || | | | |  |||||  |  |  ||| |||   |    || ||| |     || |||     ||||     |||  ||                                                                                       
GCCAGAACGCACAGGTAGTGTCACCATTGTGGGTGCAGTTTCTCCACCAGGTGGAGATTTTTCAGATCCAGTGACATCAGCTACACTTAGTATTGTCCAGgtaatctccaaattttccagcattttcatttttgcccatttcacgtctcatgagtaacaacatttagttaaaggagacacaggaaaagttt---cctagcact---------------------------------------------------------------------------------------

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 14
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag
 ||  | ||||  ||||||||||| |||||||| ||||| || |||||||| ||||| |||||||| ||||| ||  |||| |||||| ||||||| |||||   ||||||   |   |||  | |  |      |||| |  |  | ||| || | || |         ||||   |  | |  | |  | ||  || |    ||  |      | | |||||| || |   | ||  ||||   |                                        
CCCGAATCGTACTGGAAGTGTTACCATTGTTGGAGCAGTGTCCCCTCCTGGTGGAGATTTTTCAGACCCTGTCACAGCAGCTACCCTTGGTATTGTTCAGgttggtatttgtacctcctctcatccagtgcaccacattct--accagatattc-tctaagccaaagcccatgag--aagttggctatgatgttgcatgtcttccaagcgaaggaactaaagcatattgtaaatgcatgttgattag----------------------------------------

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 14
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtga-ttatttg-gttcatgt-ctgcttcc-ctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag
 ||| | ||||  ||||||||||| ||||| || ||||| || |||||||||||||| || || || ||||| ||  |||| || ||| ||||||| ||||| | | ||||| || | ||  ||| ||   |||  | | || ||  ||| || | |             |    | |   |||| |     |    | ||||        | |  | ||| |    | ||      |  |  || |||||| |       ||                            
CCCAAACCGTACAGGAAGTGTTACTATTGTCGGAGCAGTGTCTCCTCCTGGAGGAGATTTCTCGGACCCTGTCACAGCAGCTACGCTTGGTATTGTTCAGgttagtcatttgtgtacttgcactgattgtgctacatcctatcgtcaatttcagaattactcgctcaccgtagatttattgagatagca---aagcattgatcctgaatgcattt-tttatgtggttacttgaaaaatggatgtt-aaatgcatgtggagtcag---------------------------

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|124861497|gb|EH945934.1|EH945934
EST:     ATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAG                         GTCTTCTGGGGTTTGGACAAAAAGCTTGCCCAGAGAAAACATTTTCCCTCT
genomic: ATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattattt ... tcttctgcagGTCTTCTGGGGTTTGGACAAAAAGCTTGCCCAGAGAAAACATTTTCCCTCT
EST: gi|116463760|gb|EG506352.1|EG506352
EST:     GAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAG                         GTCTTCTGGGGTTTGGACAAAAAGCTTGCCCAGAGAAAACATTTTCCCTCT
genomic: GAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattattt ... tcttctgcagGTCTTCTGGGGTTTGGACAAAAAGCTTGCCCAGAGAAAACATTTTCCCTCT
EST: gi|125050950|gb|EL123219.1|EL123219
EST:     GAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAG                         GTCTTCTGGGGTTTGGAC
genomic: GAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattattt ... tcttctgcagGTCTTCTGGGGTTTGGAC
EST: gi|124832268|gb|EH916707.1|EH916707
EST:     ATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAG                         GTCTTCTGGGGTTTGGACAAAAAGCTTGCCCAGAGAAAACATTTTCCCTCT
genomic: ATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattattt ... tcttctgcagGTCTTCTGGGGTTTGGACAAAAAGCTTGCCCAGAGAAAACATTTTCCCTCT
EST: gi|116463788|gb|EG506380.1|EG506380
EST:     GAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAG                         GTCTTCTGGGGTTTGGACAAAAAGCTTGCCCAGAGAAAACATTTTCCCTCT
genomic: GAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattattt ... tcttctgcagGTCTTCTGGGGTTTGGACAAAAAGCTTGCCCAGAGAAAACATTTTCCCTCT
EST: gi|124880963|gb|EH959865.1|EH959865
EST:     GAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAG                         GTCTTCTGGGGTTTGGACAAAAAGCTTGCC
genomic: GAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattattt ... tcttctgcagGTCTTCTGGGGTTTGGACAAAAAGCTTGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA