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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgaactcttgactgctgcagtctttgcagtttattgtctcactacttttcactcaattaatagccatatgatttcagGAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCATGTCCTTGATTAAGGATCCAGATGAAAGGCGCAAAGAACAATGGGAGAAGACTGCACAA

Basic information

species Arabidopsis thaliana
transcript AT1G69340.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G69340.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G12670.1 (Glycine max), 3'ss of exon 8
---------------gttagtgaactcttgactgctgcagtctttgcagtttattgtctcactacttttcactcaattaatagccatatgattt---cagGAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCATGTCCTTGATTAAGGATCCAGATGAAAGGCGCAAAGAACAATGGGAGAAGACTGCACAA
                  | |  | |    |         | |||     || || |     ||||| |  |    |    |   || ||  ||   |||||  ||    ||| | ||| | ||||||||||||||||||||||| |||||||| || || |||||||| || |  || || |||||||| ||||  |||
gactcaatgcaaagcaaaaatttattaggaataaaaaacatatttaagtctttttataattttacttgtagcgttttcctgattaatgtggcttttacagGACTTCATCACATTTAGATACATATTTGGATCCTGCCTTCATGTCTTTGATTAAAGACCCTGATGAAAGACGTATGGAGCAGTGGGAGAAAACTGTTCAA

upper sequence: AT1G69340.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA01G06730.1 (Glycine max), 3'ss of exon 9
------------------gttagtgaactcttgactgc-tgcagtctttgcagtttattgtctcactacttttcactcaattaatagccatatgatttcagGAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCATGTCCTTGATTAAGGATCCAGATGAAAGGCGCAAAGAACAATGGGAGAAGACTGCACAA
                   |   || |||  |    || |||| | |      |||||  | | |||  |      |   | | |||        || |||||  ||     || | ||| | ||| ||||||||||||||||||| |||||||| || || |||||||| ||   ||| || |||||||| ||||  |||
ttattttcttgaaggtttttcgttgtacttgtctaagcatgcattatccatt-tttataattttacttgtagagttttcctgattagtgtggcttttacagGACTTCATCATATTTAGATACATATCTGGATCCTGCCTTCATGTCTTTGATTAAAGACCCTGATGAAAGACGTCTAGAGCAGTGGGAGAAAACTGTTCAA

upper sequence: AT1G69340.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 7
---------------gttagtgaactcttgactgc---tgcagtctttgcagtttat-tgtctcactacttttcactcaattaatagccatatgatttcagGAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCATGTCCTTGATTAAGGATCCAGATGAAAGGCGCAAAGAACAATGGGAGAAGACTGCACAA
                 || |  | ||   || |    |  | |  |||| | || |   | |   ||      |    | |    |   | || |  |||||| ||     || | ||||| ||| |||||||||| ||||||||||| ||||| ||||||||| | ||||| ||||| |||||||| || ||||| |||
gtttttatcaagaatactattccaatcacaacagaatatatattacttgctgcttttgcatttttatatgaccgatcttacttgagggtttttg-tagcagGAATTCATCATATTTGGATTCATATCTGGATCCTGCTTTCATGTCCTTAATTAAAGATCCAGATCAGAGGCGTAAAGAGCAATGGGAAAAAACTGCTCAA

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|116483352|gb|EG525944.1|EG525944
EST:     TTTCCAACTCCACTCGAGCGCCCTTCTACTGATCTTACTTTGTTACGCAG                         GAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCATGTCCTTGAT
genomic: TTTCCAACTCCACTCGAGCGCCCTTCTACTGATCTTACTTTGTTACGCAGgttagtgaac ... atgatttcagGAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCATGTCCTTGAT
EST: gi|116484633|gb|EG527225.1|EG527225
EST:     TTTCCAACTCCACTCGAGCGCCCTTCTACTGATCTTACTTTGTTACGCAG                         GAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCAT
genomic: TTTCCAACTCCACTCGAGCGCCCTTCTACTGATCTTACTTTGTTACGCAGgttagtgaac ... atgatttcagGAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCAT
EST: gi|116483396|gb|EG525988.1|EG525988
EST:     TTTCCAACTCCACTCGAGCGCCCTTCTACTGATCTTACTTTGTTACGCAG                         GAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCATGTCCTTGAT
genomic: TTTCCAACTCCACTCGAGCGCCCTTCTACTGATCTTACTTTGTTACGCAGgttagtgaac ... atgatttcagGAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCATGTCCTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcagtttattgtctcactacttttcactcaattaatagccatatgatttcagGAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCATGTCCTTGATTAAGGATCCAGATGAAAGGCGCAAAGAACAATGGGAGAAGACTGCACAA
                                aattaat  putative branch site (score: 3)
                              tcaattaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgaactcttgactgctgcagtctttgcagtttattgtctcactacttttcactcaattaatagccatatgatttcagGAACTCGAATCATCTTGATTCGTATTTGGATCCTGCCTTCATGTCCTTGATTAAGGATCCAGATGAAAGGCGCAAAGAACAATGGGAGAAGACTGCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA