Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTTACGGCTTGTTGAAATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaatgggatcaatttttttggctttggtgtgtagtttactgttgtaacaactgtcttttgcttttacttcag

Basic information

species Arabidopsis thaliana
transcript AT3G51130.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G51130.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA01G37380.1 (Glycine max), 5'ss of exon 4
AGGTTACGGCTTGTTGAAATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaatgggatcaatttttttggctttggtgtgtagtttactgttgtaacaactgtcttttgcttttacttcag
||  | |||||| |||||||||||||||| ||||| ||||||||||||||  | |||||  ||||||||||||   |   |||    |  |||| |  |     ||| ||  |    | |      | | |||| ||| ||      
AGACTGCGGCTTATTGAAATATTTGATGTAAAGCGACTTCAGATGCGCTATTCTACTTCCTTGATTGGgtgagc--atctggacttgtaattttagtatatacttgttgtaaaacactattgatgattttttttacttctag-----

upper sequence: AT3G51130.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA11G07910.1 (Glycine max), 5'ss of exon 4
AGGTTACGGCTTGTTGAAATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaatgggatcaatttttttggctttggtgtgtagtttactgttgta-acaactgtcttttgcttttacttcag-
|| || || ||| |||||||||||||||| ||||| ||||||||| ||||  | |||||  |||||||||||||  | |||||       || |   ||| || | ||  ||  |||   | || | ||  | ||  || ||||||   
AGATTGCGCCTTATTGAAATATTTGATGTAAAGCGACTTCAGATGTGCTATTCTACTTCCTTGATTGGgtgagt--attgggac------ttgtaattttagtatata-cttgttgtaaaacactattgattgttttttctacttctag

upper sequence: AT3G51130.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv04s0023g02970.t01 (Vitis vinifera), 5'ss of exon 4
AGGTTACGGCTTGTTGAAATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagt---cgaatgggatcaatttttttggctttg-gtgtgtagtttactgttgtaacaactgtcttttgcttttacttcag
||| |||| ||| | || || ||||||||||| |||||||| |||||||| ||||||||| |||||||||| ||   | | |    | |||||| ||  || || |  | ||  ||| | |||         || |    | | | |||||
AGGCTACGCCTTATCGAGATTTTTGATGTCAAACGGCTTCAAATGCGCTATGCCACTTCTCTGATTGGgtgggtgctcaatttaccttaattttcttatctatgtgcttataagttattcttg--------atcctcatttctaatttcag

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|86040772|gb|DR336527.1|DR336527
EST:     ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGG                         GGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGACC
genomic: ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaa ... tttacttcagGGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGACC
EST: gi|86040774|gb|DR336529.1|DR336529
EST:     ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGG                         GGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGACC
genomic: ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaa ... tttacttcagGGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGACC
EST: gi|86040770|gb|DR336525.1|DR336525
EST:     ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGG                         GGGTCCATCAACTCT
genomic: ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaa ... tttacttcagGGGTCCATCAACTCT
EST: gi|86040779|gb|DR336534.1|DR336534
EST:     ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGG                         GGGTCCATTCAACTCTGGCAACGTTTGTGGCTGTTTATGCACT
genomic: ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaa ... tttacttcagGGGTCCAT-CAACTCTGGCAACGTTTGTGGCTGTTTATGCACT
EST: gi|164091229|gb|EL994210.1|EL994210
EST:     ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGG                         GGGTCCATCAACTCTGGCAACGTTTGTGGCTG
genomic: ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaa ... tttacttcagGGGTCCATCAACTCTGGCAACGTTTGTGGCTG
EST: gi|86040778|gb|DR336533.1|DR336533
EST:     ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTNG                         GGGTCCATCAACTCTGGCAACGTTTGT
genomic: ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaa ... tttacttcagGGGTCCATCAACTCTGGCAACGTTTGT
EST: gi|86040777|gb|DR336532.1|DR336532
EST:     ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGG                         GGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGACC
genomic: ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaa ... tttacttcagGGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGACC
EST: gi|86040776|gb|DR336531.1|DR336531
EST:     ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGG                         GGGGTCCATCAACTCTGGCAACGTTTGGGGGCTGTTTATGCNCTTTTTGGA
genomic: ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaa ... tttacttcagGGG-TCCATCAACTCTGGCAACGTTTGTGG-CTGTTTATGCACTTTTTGGA
EST: gi|86040771|gb|DR336526.1|DR336526
EST:     ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGG                         GGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGACC
genomic: ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaa ... tttacttcagGGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGACC
EST: gi|86040773|gb|DR336528.1|DR336528
EST:     ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGG                         GGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGACC
genomic: ATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaa ... tttacttcagGGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGACC
EST: gi|125231529|gb|EL245614.1|EL245614
EST:     TATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGG                         GGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGA
genomic: TATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaa ... tttacttcagGGGTCCATCAACTCTGGCAACGTTTGTGGCTGTTTATGCACTTTTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTTACGGCTTGTTGAAATATTTGATGTCAAGCGGCTTCAGATGCGCTACGCCACTTCTATGATTGGgtgagtcgaatgggatcaatttttttggctttggtgtgtagtttactgttgtaacaactgtcttttgcttttacttcag

- - - - - - - - - - - - - - - - - - -  CAGATG