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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcatttgggcatgctattcttttcattttctaacttttggttttgttgttgctactatgactgattactcttatttggtatgaatcggcattttagGATACTTTTAGGGGAAGATTGTGTGAGTGCCCTACTGTTCAAGGTGTTAAATTCGTTGGTGACGGTTACACTCACTGCAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G52850.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 6
gtatcatttgggcatgctattcttttcattttctaacttttggttttgttgttgctactatgactgattactcttatttggtatgaatcggcat-tttagGATACTTTTAGGGGAAGATTGTGTGAGTGCCCTACTGTTCAAGGTGTTAAATTCGTTGGTGACGGTTACACTCACTGCAAAG
                        |   | || |    ||   || |   |   ||  |    |||  ||  | |||      ||  |  | |  | ||||| |||||| | |||||| | ||||| || ||   |||  ||||||||||||| |||||||| || |||||||||||  |||
-----------------------gtatttcttatggtgttatcttcttcagaaacttttccatctggctatgcatatcatacttggctgtgtacgtgtagGACACTTTTCGTGGAAGAGTTTGTGAATGTCCAGTTGTGAAAGGTGTTAAATTTGTTGGTGATGGCTACACTCACTGTGAAG

upper sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 6
gtatcatttgggcatgctattcttttcattttctaacttttggttttgttgttgctactatgactgattactcttatttggtatgaatcggcat-tttagGATACTTTTAGGGGAAGATTGTGTGAGTGCCCTACTGTTCAAGGTGTTAAATTCGTTGGTGACGGTTACACTCACTGCAAAG
                        |   | || |    ||   || |   |   ||  |    |||  ||  | |||      ||  |  | |  | ||||| |||||| | |||||| | ||||| || ||   |||  ||||||||||||| |||||||| || |||||||||||  |||
-----------------------gtatttcttatggtgttatcttcttcagaaacttttccatctggctatgcatatcatacttggctgtgtacgtgtagGACACTTTTCGTGGAAGAGTTTGTGAATGTCCAGTTGTAAAAGGTGTTAAATTTGTTGGTGATGGCTACACTCACTGTGAAG
















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|164078106|gb|ES182389.1|ES182389
EST:     GGCAAGACAAAAGCTG-CAACATTACTGCATGCAGG                         GATACTTTTAGGGGAAGATTGTGTGAGTGCCCTACTGTTCAAGGTGTTAAA
genomic: GGCAAGAC-AAAGCTGCCAACATTACTGCATGCAGGgtatcatttg ... ggcattttagGATACTTTTAGGGGAAGATTGTGTGAGTGCCCTACTGTTCAAGGTGTTAAA
EST: gi|124731250|gb|EH822652.1|EH822652
EST:     ACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG                         GATACTTTTAGGGGAAGATTGTGTG
genomic: ACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGGgtatcatttg ... ggcattttagGATACTTTTAGGGGAAGATTGTGTG
EST: gi|164090512|gb|ES003141.1|ES003141
EST:     CGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG                         GATACTTTTAGGGGAAGATTGTGTGAGTGCCCTACTGTTCAAGGTGTTAAA
genomic: CGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGGgtatcatttg ... ggcattttagGATACTTTTAGGGGAAGATTGTGTGAGTGCCCTACTGTTCAAGGTGTTAAA
EST: gi|86037686|gb|DR333441.1|DR333441
EST:     ACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG                         GATAC-TTTAGGGGAAGATTGTGTGAGTGCCCTACTGTTCAAGGTGTTAAA
genomic: ACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGGgtatcatttg ... ggcattttagGATACTTTTAGGGGAAGATTGTGTGAGTGCCCTACTGTTCAAGGTGTTAAA
EST: gi|125301176|gb|EL315261.1|EL315261
EST:     ACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG                         GATACTTTTAGGG-AAGATTGTGTGAGTG
genomic: ACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGGgtatcatttg ... ggcattttagGATACTTTTAGGGGAAGATTGTGTGAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttgttgctactatgactgattactcttatttggtatgaatcggcattttagGATACTTTTAGGGGAAGATTGTGTGAGTGCCCTACTGTTCAAGGTGTTAAATTCGTTGGTGACGGTTACACTCACTGCAAAG
                 gactgat  putative branch site (score: 3)
                           tcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcatttgggcatgctattcttttcattttctaacttttggttttgttgttgctactatgactgattactcttatttggtatgaatcggcattttagGATACTTTTAGGGGAAGATTGTGTGAGTGCCCTACTGTTCAAGGTGTTAAATTCGTTGGTGACGGTTACACTCACTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG