Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttttttcttaagtaatctgcggtttgtgtcttaaaaaaatttcatgaattcttgttttcaatagtttttctgatttcctcttctgtttctgtccagGAAAGTGAAGTGAAGTGGGCATCTAGATGGGATACTTATCTTCTGATGAGTGATAACCAAATCCACTGGTTCTCTATCGTCAATTCTCTGATGATCGTCC

Basic information

species Arabidopsis thaliana
transcript AT5G10840.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 6
gcaagttttttcttaagtaatctgcggtttgtgtcttaaaaaaatttcatgaattcttgttttcaatagtttttctgatttcctctt----ctgtttctgtccagGAAAGTGAAGTGAAGTGGGCATCTAGATGGGATACTTATCTTCTGATGAGTGATAACCAAATCCACTGGTTCTCTATCGTCAATTCTCTGATGATCGTCC
   | | |||  |  |   |  ||  ||     ||||        | |    |||||  | ||    |  || | |||  | || ||     ||  |   | ||||| ||||| ||||||||||| || ||||||||| | ||| | |||||||||||| ||||||| ||||||||||| || || || ||  ||||||| || |
--tattgtttcttccatccaagtggagtc---atcttcctcttcctcctcttattctcatctttgtcatcttctttgacctgcttttacctttgcctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC

upper sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G06460.1 (Glycine max), 3'ss of exon 6
-gcaagttttttcttaagtaatctgcggtttgtgtcttaaaaaaatttcatgaattcttgttttcaatagtttttctgatttcctcttctgtttctgtccagGAAAGTGAAGTGAAGTGGGCATCTAGATGGGATACTTATCTTCTGATGAGTGATAACCAAATCCACTGGTTCTCTATCGTCAATTCTCTGATGATCGTCC
  | |   |  || |   |  | |  | | | | |  |||||     | |||   | |  || | | ||  |  | |  |  | |  |||| | |  | ||||| ||||| ||||||||||| || ||||||||| ||||| | || |||| |||| | |||||||||||||||||||| || || ||  | ||||| || |
aactaacatcctcatcttttttttttgttgt-tatgataaaatgtgattatgggctgtatttcttattatctgctattttgcctttgtctggtacc-ttcagGAGAGTGACGTGAAGTGGGCTTCAAGATGGGATGCTTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCTATTGTTAACTCATTAATGATTGTTC

upper sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G11780.1 (Glycine max), 3'ss of exon 6
gcaagttttttcttaagtaatctgcggt-ttgtgtcttaaaaaaatttcatgaattcttgttttcaatagtttttctgatttcctctt----ctgtttctgtccagGAAAGTGAAGTGAAGTGGGCATCTAGATGGGATACTTATCTTCTGATGAGTGATAACCAAATCCACTGGTTCTCTATCGTCAATTCTCTGATGATCGTCC
      |        ||| | || |    |  | |  |        |||    |||||  | ||    |  || | |||  | |  ||     ||  |   | ||||| ||| | ||||||||||| || ||||||||| | ||| | |||||||||||| ||||||| ||||||||||| || || || ||  ||||||| || |
------tccaaggggagtcaccttcctcatcctattctcctcttccttctcttattctcatctttgtcatcttctttgacctgcctttacctttgcctacattcagGAGAGTAATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC

upper sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G06420.1 (Glycine max), 3'ss of exon 6
gcaagttttttcttaagtaatctgcggtttgtgtcttaaaaaaatttcatgaattcttgttttcaatagtttttctgatttcctcttctgtttctgtccagGAAAGTGAAGTGAAGTGGGCATCTAGATGGGATACTTATCTTCTGATGAGTGATAACCAAATCCACTGGTTCTCTATCGTCAATTCTCTGATGATCGTCC
   ||  ||    | |     ||    ||  |||  | | ||||| | ||       ||| ||   || | | |   ||| ||| |      |   | ||||| ||||| ||||||||||| || ||||||||| | ||| | || |||| |||| | ||||||||||||||||| || || || ||  | ||||| || |
-agagaattaatgttatccgcctttttttgttgttatgataaaatgtgattgtgggctgtatttcttattatctgctattgcctttggctggtaccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCAATTGTTAACTCATTAATGATTGTTC

upper sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0008g06640.t01 (Vitis vinifera), 3'ss of exon 6
----gcaagttttttcttaagtaatctgc-ggtttgtgtcttaaaaaaatttcatgaattcttgttttcaatagtttttctgatttcctcttctgtttctgtccagGAAAGTGAAGTGAAGTGGGCATCTAGATGGGATACTTATCTTCTGATGAGTGATAACCAAATCCACTGGTTCTCTATCGTCAATTCTCTGATGATCGTCC
     |||||||  |  |  || |   ||    |||  | ||       ||      ||| |  || | | | ||||||    ||| ||| |||  | |  | ||||||||||| |||||||||||||||||||||||||| |||||||| ||||||||| |||| |||||||||||||| || || |||||| ||||||| || |
ttaaccaagtttaataattggtgaaaagccaacttgcttgttgcccctgttaaggttattatgattctta-tggttttt----ttttctcatct-ctgccatacagGAAAGTGATGTGAAGTGGGCATCTAGATGGGATACCTATCTTCTCATGAGTGATGACCAGATCCACTGGTTCTCAATTGTTAATTCTTTGATGATTGTTC

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|86084840|gb|DR380599.1|DR380599
EST:     AAGTTGAACAAAAGAAGGAGATTATCTTCACATATGACGTCGATTTCCAG                         GAAAGTGAAGTGAAGTGGGCATCTAGATGGGATACTTATCTTCTGATGAGT
genomic: AAGTTGAACAAAAGAAGGAGATTATCTTCACATATGACGTCGATTTCCAGgcaagttttt ... ttctgtccagGAAAGTGAAGTGAAGTGGGCATCTAGATGGGATACTTATCTTCTGATGAGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgaattcttgttttcaatagtttttctgatttcctcttctgtttctgtccagGAAAGTGAAGTGAAGTGGGCATCTAGATGGGATACTTATCTTCTGATGAGTGATAACCAAATCCACTGGTTCTCTATCGTCAATTCTCTGATGATCGTCC
                          ttctgat  putative branch site (score: 3)
                       tttttctgatttcctc  CT-rich tract
             ttttcaatagttttt  TA-rich tract