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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTCGAATATCCCAAATTCGATCCGTTTTCCGGCGATAATCTCCGATCTAGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataactttcatctatatccgattagatcgtgtaacttctagatctctggctagtgaatcgcttgctgaatctagtcagatctctgcatagtatctggt...

Basic information

species Arabidopsis thaliana
transcript AT1G04410.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04410.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA02G00810.2 (Glycine max), 5'ss of exon 1
AAGTCGAATATCCCAAATTCGATCCGTT---TTCCGGCGATAATCTCCGATCTAGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataactttcatctatatccgattagatcgtgtaacttctagatctctggctagtgaatcgcttgct-gaatctagtcagatctctgcatagtatctggt--
   ||     ||      || |  |  |   ||||  ||||    |||  |         ||||| ||||| |||||||| || ||||| |||||||||||||||||  || |||||   ||   ||    ||   |   | ||  || |   | |      ||| | ||| || | ||  |   | | ||  |   ||  |    
---TCACTCTTCTTCGTCTCAAATCTCTTCGTTCCTTCGATTCGTTCCATTTCTTCCAAAATGGCCAAAGACCCAGTTCGCGTTCTCGTCACTGGAGCTGCAGgtatttctctcatcgccat--aatctcttctcttccgtgcttaattttcagatt-catctcgatcgcttgattttacacccttttgtgttttcaatgcgagat

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv07s0005g03350.t01 (Vitis vinifera), 5'ss of exon 2
AAGTCGAATATCCCAAATTCGATCCGTTTTCCGGCGATAATCTCCGATCTAGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataactttcatctatatccgattagatcgtgtaacttctagatctctggctagtgaatcgc--ttgctgaatctagtcagatctctgcatagtatctggt
                  ||| |    | ||| | | |   || ||||    |  | ||||| |||||||||||||| || |||||||||||||| |||||||  ||    |||||        |    | ||   |  ||   |   ||   ||  |       ||| |   | | ||   || | ||  |  | | |  |
---------------GCGTCGTTTTCCTCTCCCGTGCTCCCCTGCGATTCCTA--CAATGGCCAAAGAACCAGTTCGCGTTCTCGTTACTGGAGCCGCAGgtaccacaag-atctacggttctcttctccatgattccgctgtttggttgctcagaaagcaagagttgttctgttttgttttattt-tgttttttctttttt

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv07s0005g03360.t01 (Vitis vinifera), 5'ss of exon 1
-AAGTCGAATATCCCAAATTCGATC-CGTTTTCCGGCGATAATCTCCGATCTAGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataactttcatctatatccgattagatcgtg---taacttctagatctctggctagtgaatcgcttgctgaatctagtcagatctctgcatagtatctggt
 |  |   || | |     ||| |  ||| | ||  |      || ||||    |  | ||||| |||||||||||||| || |||||||||||||| |||||||| ||    ||||||  |    |   || ||   | |||  | | |  || |  |    |    ||| |   | | ||    | | | | |  | | | ||
CAGATTAGATTTGCAGGCGTCGTTTTCGTCTCCCTTCCTCTTCCTACGATTCTTA--CAATGGCCAAAGAACCAGTTCGCGTTCTCGTTACTGGAGCCGCAGgtattacgag-atctatggctctcttcttcatggtttcactgtttggttgctcggaaagcgaagatttgttttgttttgttt--ttttttctttcttttttgt

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|125296611|gb|EL310696.1|EL310696
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATT
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATT
EST: gi|47829836|gb|CK119520.1|CK119520
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|47830669|gb|CK120353.1|CK120353
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|164092215|gb|ES208898.1|ES208898
EST:     CTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCA
genomic: CTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCA
EST: gi|47828241|gb|CK117925.1|CK117925
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|301503095|gb|HO208635.1|HO208635
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|47829133|gb|CK118817.1|CK118817
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|47829241|gb|CK118925.1|CK118925
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|125040609|gb|EL112878.1|EL112878
EST:     TGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: TGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|124818772|gb|EH903638.1|EH903638
EST:     TTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: TTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|47828264|gb|CK117948.1|CK117948
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|47832292|gb|CK121976.1|CK121976
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|125191204|gb|EL206158.1|EL206158
EST:     TCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATG
genomic: TCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATG
EST: gi|125043764|gb|EL116033.1|EL116033
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATA
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATA
EST: gi|301501445|gb|HO206985.1|HO206985
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|47828810|gb|CK118494.1|CK118494
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
EST: gi|47831346|gb|CK121030.1|CK121030
EST:     AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAG                         GACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG
genomic: AGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataacttt ... gattatgcagGACAAATCGGATATGCTCTTGTACCTATGATTGCAAGGGGTATCATGCTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTCGAATATCCCAAATTCGATCCGTTTTCCGGCGATAATCTCCGATCTAGATCCGATGGCGAAAGAACCAGTTCGTGTGCTCGTTACTGGAGCTGCAGgtataactttcatctatatccgattagatcgtgtaacttctagatctctggctagtgaatcgcttgctgaatctagtcagatctctgcatagtatctggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcgcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagatctc