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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacttatatattttattttggccttaattttaatcgatgtgagatttggattttttccaataattcacgaacattaaagcttaatttttcatttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG

Basic information

species Glycine max
transcript GLYMA15G11350.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G11350.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------------------ccacttatatattttattttggccttaattttaatcgatgtgagatttggattttttccaataattcacgaacattaaagcttaatttttcatttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG
                                                                  | | |  ||    || | | |||  | |   || ||    || |   || ||  ||   |  | || |     | |||  | |    | |     | |||||||| || |||||||| || |||||||||||||| ||||||||| ||||| | || || || |||||||| ||  | || |||
gtacgagattagtacaagcattatacttggtttttggttttctacaccatcgttaggggtgcaggacaaatcttagggattttctgggctctgaaaatagtcttcttggg---tgcatactt---agaagttgagttttagtaattcctctcgtatggacctgcagGTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGTTTGTTCACCTTTACTGCTGCTTATTTACCTTGG

upper sequence: GLYMA15G11350.2 (Glycine max), 3'ss of exon 3
lower sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 3
ccacttatatattttattttggccttaattttaatcgatgtgagatttggattttttccaataattcacgaacattaaagcttaatttttcatttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG
                    |    ||| ||   |       | || |   |    || ||  ||   |     ||| ||  |    ||   ||   ||||| || || ||||||||||||||||| |  ||||||||||| ||||| ||||| || || ||||| || || ||||| ||||||
--------------------gttggtaacttctgtttcccacaaatctaagtcgcctctaaatatcagc-----ttatagtct---cttgtgttccacagGTCTATGTATGGAGCAAACAAAATCCTTATATTCACATGAGTTTCCTTGGTCTGTTCACCTTCACAGCAGCTTACCTACCATGG
















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|15287660|gb|BI471551.1|BI471551
EST:     AGTCGTTTGCAAAAATAATATTCCTTAGCAACTCATTGACATTTATGATG                         GTTTACGTGT-GAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
genomic: AGTCGTTTGCAAAAATAATATTCCTTAGCAACTCATTGACATTTATGATGgtaagtcaca ... catttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
EST: gi|58023286|gb|CX710027.1|CX710027
EST:     AGTCGTTTGCAAAAATAATATTCCTTAGCAACTCATTGACATTTATGATG                         GTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
genomic: AGTCGTTTGCAAAAATAATATTCCTTAGCAACTCATTGACATTTATGATGgtaagtcaca ... catttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
EST: gi|151400841|gb|EV270655.1|EV270655
EST:     AGTCGTTTGCAAAAATAATATTCCTTAGCAACTCATTGACATTTATGATG                         GTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
genomic: AGTCGTTTGCAAAAATAATATTCCTTAGCAACTCATTGACATTTATGATGgtaagtcaca ... catttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
EST: gi|23731152|gb|BU763683.1|BU763683
EST:     AAATAATATTCCTTAGCAACTCATTGACATTTATGATG                         GTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
genomic: AAATAATATTCCTTAGCAACTCATTGACATTTATGATGgtaagtcaca ... catttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
EST: gi|213608886|gb|DB980784.1|DB980784
EST:     CTTAGCAACTCATTGACATTTCCGATG                         GTTTACGTG-GCCTGCAAACAAATTTCCTTCATTCACATGAGCTTCCTGGG
genomic: CTTAGCAACTCATTGACATTTATGATGgtaagtcaca ... catttttcagGTTTACGTGTG-GAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGG
EST: gi|151397563|gb|EV267436.1|EV267436
EST:     AGTCGTTTGCAAAAATAATATTCCTTAGCAACTCATTGACATTTATGATG                         GTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
genomic: AGTCGTTTGCAAAAATAATATTCCTTAGCAACTCATTGACATTTATGATGgtaagtcaca ... catttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
EST: gi|214006459|gb|DB987212.1|DB987212
EST:     ATTGACATTTATGATG                         GTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
genomic: ATTGACATTTATGATGgtaagtcaca ... catttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
EST: gi|58016888|gb|CX703630.1|CX703630
EST:     AGTCGTTTGCAAAAATAATATTCCTTAGCAACTCATTGACATTTATGATG                         GTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT
genomic: AGTCGTTTGCAAAAATAATATTCCTTAGCAACTCATTGACATTTATGATGgtaagtcaca ... catttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggattttttccaataattcacgaacattaaagcttaatttttcatttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG
                                  gcttaat  putative branch site (score: 4)
                                        tttttcatttttc  CT-rich tract
                         aacattaaagcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacttatatattttattttggccttaattttaatcgatgtgagatttggattttttccaataattcacgaacattaaagcttaatttttcatttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
ccactta
- - - - - - - - - - -gccttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacgaac