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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaaactaaactctctttagttctcaatgtgtcttgcacattggcctaaccagtaagaggattggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG

Basic information

species Arabidopsis thaliana
transcript AT3G56940.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 3
-------------------gtaat-taaactaaactctctttagt-tctcaatgtgtcttgcacattggcctaa--ccagtaagaggattggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG
                   || |  |  |  ||  |    ||| | | | |||   ||||     ||     ||     ||      ||| |   | ||||||||||| |||||||| |||||||| |||||| | ||   ||||||||| || || ||  | |||||||| || || || ||||||||||| ||||||
gccgaaacagatcatgtttgtcacatctatcaacataaagttactgttttaatccttcttaactgttacttaaaacttggttgtcaaatttgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATTATCGAG

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------------------------gtaattaaactaaactctctttagttctcaatgtgtcttgcacattggcctaaccagtaagaggattggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG
                                                                            ||  |||||       ||  |       |  || |  |       |   || |  | |      ||| |  || ||||||||||| ||||||||||||||||| |||||  | ||  ||||||| || || || ||| | |||||||| || || || |||||||| ||||| |||
gtaattatagtataataagtttctacattcaattgtatactagattgcaaatattatcttaattttttaccctagtgtgtttaaatctttggcttctcgagaacctctgggattcctctggtcctcttatgacttcccaaatttgtcttgcagGTTTATGTAACAATGTACCTCAATGATTGCCAGCGTACGGATTTCTATGAAGGAATTGGGCTCAACACAAAAGAATTTGACATGCATGTGATCATAGAG

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ28505 (Selaginella moellendorffii), 3'ss of exon 3
gtaattaaactaaactctctttagttctcaatgtgtcttgcacattggcctaaccagtaagaggattggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG
     ||||  ||||   |||| | |||   ||    ||  | ||  ||  |  |  |       |||   || ||||| || |||||||||||||| ||||||||||||||||||   || ||||| || || ||  |  |||| || || ||||| ||||||||||||||||||
----gtaaagcaaac---ctttggctcttcttggaatttttagat--gctcatgc--ttccgctcttgctcttccagGTGTACGTGACAATGTACCTAAATGACTGCCAAAGAACTGCCTTTTACGAAGGAATAGGCCTCGACACTAAAGATTTCGACATGCATGTCATCATCGAG

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|124934763|gb|EL011807.1|EL011807
EST:     TCCTCAATGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCG                         GTTTATGTGACAATGTA
genomic: TCCTCAATGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCGgtaattaaac ... ggctttacagGTTTATGTGACAATGTA
EST: gi|124746737|gb|EH837049.1|EH837049
EST:     TCCTCAATGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCG                         GTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTT
genomic: TCCTCAATGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCGgtaattaaac ... ggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTT
EST: gi|125310220|gb|EL324305.1|EL324305
EST:     TGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCG                         GTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTA
genomic: TGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCGgtaattaaac ... ggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTA
EST: gi|124933260|gb|EL010435.1|EL010435
EST:     CAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCG                         GTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAG
genomic: CAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCGgtaattaaac ... ggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAG
EST: gi|124883839|gb|EH962741.1|EH962741
EST:     GCTCTGGTCTCGCTTCTTCTGCCTCTCGG                         GTTTATGTGACAATGTACCTCAATAGACTGCCAAAGAACTAATTTCTACG
genomic: GCTCTGGTCTCGCTTCTTCTGCCTCTC-Ggtaattaaac ... ggctttacagGTTTATGTGACAATGTACCTCAAT-GACTGCCAAAGAACTAATTTCTACG
EST: gi|125047522|gb|EL119791.1|EL119791
EST:     CAATGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCG                         GTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAG
genomic: CAATGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCGgtaattaaac ... ggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAG
EST: gi|124940070|gb|EL016555.1|EL016555
EST:     CTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCG                         GTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAG
genomic: CTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCGgtaattaaac ... ggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAG
EST: gi|124823977|gb|EH908843.1|EH908843
EST:     CCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCG                         GTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAG
genomic: CCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCGgtaattaaac ... ggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAG
EST: gi|163983150|gb|ES111796.1|ES111796
EST:     CCTTCAATGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCG                         GTTTATGTGACAA
genomic: CC-TCAATGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCGgtaattaaac ... ggctttacagGTTTATGTGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctcaatgtgtcttgcacattggcctaaccagtaagaggattggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG
                         gcctaac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaaactaaactctctttagttctcaatgtgtcttgcacattggcctaaccagtaagaggattggctttacagGTTTATGTGACAATGTACCTCAATGACTGCCAAAGAACTAATTTCTACGAGGGTATCGGGTTAAACACAAAGGAGTTCGATATGCATGTCATCATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG