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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcttcctctcctcgtctccttcttttggaattttacaagttgtgagatttgttgtattgatttaagtaatttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTAGGTAGATCTTTCGAAGACATGTGTGCTCAAATGTATTACCGAGGCAAGATGT

Basic information

species Arabidopsis thaliana
transcript AT1G01090.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G033894_T01 (Zea mays), 3'ss of exon 1
----gtacgcttcctctcctcgtctccttcttttggaatttta--caagttgtgaga---tttgttgtat---tgatttaag-----taatttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTAGGTAGATCTTTCGAAGACATGTGTGCTCAAATGTATTACCGAGGCAAGATGT
    | |   |  ||    |  | | ||  |  || || | |   |||||||    |   | |||||| |   | ||| | |     |  |||     ||  | | |||   || || | | ||||| ||||||| || ||| | || ||  |    ||||| ||||||||||| |||||||| ||||| ||||||||||
acatggaaaatgtcttatttgtttttctgttgctgcaagtctgttcaagttgcagaacactgtgttgtgtacgtaattcatggtctatcgttttctccagGCGGTTACCCGGGAAGAGGCACTGGAGCTGTATGAGGACATGGTTCTTGGCCGTGTATTCGAGGACATGTGTGCACAAATGTACTACCGTGGCAAGATGT

upper sequence: AT1G01090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G44930.1 (Glycine max), 3'ss of exon 1
-----------------gtacgcttcctctcctcgtctccttcttttggaattttacaagt-tgtgagatttgttgtattgatttaagtaatttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTAGGTAGATCTTTCGAAGACATGTGTGCTCAAATGTATTACCGAGGCAAGATGT
                 |  |  ||    ||    |     ||||||| || |  | |||| | ||||| |  |  | ||  |||   |   |      || | || || ||||||||||| ||| || | |||||||| ||| || |||| || || || |||||||||||||| || ||||||||  ||||||| ||||
atcttcttatgccatctgcccatttagcttcagatttgttgtcttttgtaaata-ataagtgtttgagactattgttttttgtttgtatctgtgtgtgcagCTTATTACGAAAGAGGAAGGTTTGCAGCTCTATGAAGACATGGTATTAGGCAGGTCCTTTGAAGACATGTGTGCCCAGATGTATTATAGAGGCAAAATGT

upper sequence: AT1G01090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G02090.1 (Glycine max), 3'ss of exon 1
---------gtacgcttcctctcctcgtctccttct--tttggaattttacaagttgtgagatttgttg------tattgatttaagtaatttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTAGGTAGATCTTTCGAAGACATGTGTGCTCAAATGTATTACCGAGGCAAGATGT
           |   ||  | |  |  |    | ||  |||||||||||     | |    |  ||||       |||||||||       |    | || |  | || ||||||||||| |||||| | ||||||||||||||| |||| || |  || || |||| ||||||| | ||||||||  | ||||| ||||
gattatggaaaatagttggtgttgtgctacagtactgatttggaattttttgtttgggagtaagtgttttgagattattgattttgtctggtgagtacagCTTGTTACAAAAGAGGAAGGGTTGGAGCTCTATGAAGATATGATATTAGGGAGGTTCTTTGAGGACAAGTGTGCTGAGATGTATTATAGGGGCAAAATGT

upper sequence: AT1G01090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0048g02580.t01 (Vitis vinifera), 3'ss of exon 1
-----------gtacgcttcctct--cctcgtctccttcttttggaattttacaagttgtgagatttgttgtattgatttaagtaatttgaaat-----agTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTAGGTAGATCTTTCGAAGACATGTGTGCTCAAATGTATTACCGAGGCAAGATGT
           | |   | |   |    |||| | ||| | ||  | |||  ||| ||   | |       || |  ||   ||  |||    |     || |||| || |  |||||||| |||||| |||||||||| ||| || | |||||| |||| || |||||||||||||| ||||| ||| | ||||| ||||
gagaattgcgagaattgtgcaaatggtttcgtttacttttcttacattttctcaa-ttaccaaacagagcataatctttcgtgtctttttgtctgtttcagCTGATTACGAGGGAGGAAGGGTTGGAGCTGTATGAAGACATGGTATTGGGTAGAGCTTTTGAGGACATGTGTGCTCAGATGTACTACAGGGGCAAAATGT

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|125037188|gb|EL109457.1|EL109457
EST:     CTGTCCAGGAAGTTGTCGAGGAGAAGCAATCCACCAATAATACCAGCCTG                         TTGATAACCAAAAGAGGAAGGATTGGAGTTGTA
genomic: CTGTCCAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTGgtacgcttcc ... tttgaaatagTTGATAACCAAA-GAGGAAGGATTGGAGTTGTA
EST: gi|125078654|gb|EL140961.1|EL140961
EST:     AATCCACCAATAATACCAGCCTG                         TTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTA
genomic: AATCCACCAATAATACCAGCCTGgtacgcttcc ... tttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTA
EST: gi|164016181|gb|ES077188.1|ES077188
EST:     CTGTCCAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTG                         TTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATG
genomic: CTGTCCAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTGgtacgcttcc ... tttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATG
EST: gi|86052450|gb|DR348207.1|DR348207
EST:     CTGTCCAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTG                         TTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTAGGT
genomic: CTGTCCAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTGgtacgcttcc ... tttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTAGGT
EST: gi|86052460|gb|DR348217.1|DR348217
EST:     CTGTCCAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTG                         TTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTAGGT
genomic: CTGTCCAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTGgtacgcttcc ... tttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTAGGT
EST: gi|124914637|gb|EH988511.1|EH988511
EST:     CTGTCCAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTG                         TTGATAACCAAAGAGGAAGGATTG
genomic: CTGTCCAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTGgtacgcttcc ... tttgaaatagTTGATAACCAAAGAGGAAGGATTG
EST: gi|86052445|gb|DR348202.1|DR348202
EST:     TGTCCAGGAAGTTGTCAAGGGAGAAGCAATNCACCAATAATACCCNCCTG                         TTGATAACCCAAGAGGAAGGATTGGAGT
genomic: TGTCCAGGAAGTTGTCAAGG-AGAAGCAATCCACCAATAATACCAGCCTGgtacgcttcc ... tttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGT
EST: gi|125284736|gb|EL298821.1|EL298821
EST:     CTGTCCAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTG                         TTGATAACCAAAGAGGAAGGATTGGAGTTGTA
genomic: CTGTCCAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTGgtacgcttcc ... tttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTA
EST: gi|125324197|gb|EL338277.1|EL338277
EST:     TGTCCAAGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTG                         TTGATAACCAAAGAGGAAGGATTGGAGTT
genomic: TGTCC-AGGAAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTGgtacgcttcc ... tttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTT
EST: gi|124780625|gb|EH870568.1|EH870568
EST:     AAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTG                         TTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTA
genomic: AAGTTGTCAAGGAGAAGCAATCCACCAATAATACCAGCCTGgtacgcttcc ... tttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaattttacaagttgtgagatttgttgtattgatttaagtaatttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTAGGTAGATCTTTCGAAGACATGTGTGCTCAAATGTATTACCGAGGCAAGATGT
                              tattgat  putative branch site (score: 3)
                           ttgtattgatttaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcttcctctcctcgtctccttcttttggaattttacaagttgtgagatttgttgtattgatttaagtaatttgaaatagTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATATGATACTAGGTAGATCTTTCGAAGACATGTGTGCTCAAATGTATTACCGAGGCAAGATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG