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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAAgtatgtcttttaactgttctcctttcattcagggtgattcggaaaacctcatacataataatttcttttggagatctctgttagttatctgtctttggat...

Basic information

species Glycine max
transcript GLYMA03G39290.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39290.1 (Glycine max), 5'ss of exon 23
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 22
GTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAAgtatgtcttttaactgttctcctttcattcagggtgattcggaaaacctcatacataataatttcttttggagatctctgttagttatctgtctttggat------
|| ||||| ||| ||||||| || ||||| ||  | ||||||||||| ||||| ||| |||| ||||||||||| |||||||||||||||||||| |||    ||  |   | |||||||||    ||       |     | |  || |   ||| ||| | ||| |||| |||      | | || |||||  |      
GTAAAATCAAAACTGAAGGGACACCAAAAACGCGTAACTGGTTTAGCTTTTTCCACCAGTCTAAACATCCTGGTCTCATCTGGTGCTGATGCTCAGgta--atttgaaggggctctcctttcgaaaagaaaagcac----catccaatgccagatagtttttcttgaagatttcttgactctttttggctttgactttggtt

upper sequence: GLYMA03G39290.1 (Glycine max), 5'ss of exon 23
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 22
GTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAAgta------tgtcttttaactgtt-----ctcctttcattcagggtgattcggaaaacctcatacataataatttcttttg----gagat---ctctgttagttatctgtctt-tggat-------------
||||||   || |||||||||||||||||| |||||||||| ||||| || || | |  ||| ||  | || || ||||| || || |||||||| |||      |||   | || ||       ||   |   | ||   |||| | |  |   || |    ||    | || | |    | |||   | |    || | | | |||   | ||             
GTGAAAAGCAAGTTGAAGGGTCATCAAAAGAGAATTACTGGCTTAGCTTTCTCTAACACTCTCAATGTTCTTGTATCATCCGGAGCGGATGCTCAGgtacatacttgttcatcaattgcatacagctgtctatttgcactttgatccagctattttcgtgtgaaactcgtgctctggtcccgggatggacccgtccagatctttatctgacgcatttcttctttccag
















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|163917881|gb|EH039022.1|EH039022
EST:     CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA                         CTTTGTGTATGGAGTATTGATACATGGGAGAAGAGAAAATCAGTTCCTATA
genomic: CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAAgtatgtcttt ... ttccatacagCTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
EST: gi|254343985|gb|GR857741.1|GR857741
EST:     CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA                         CTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
genomic: CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAAgtatgtcttt ... ttccatacagCTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
EST: gi|193540955|gb|FK496089.1|FK496089
EST:     CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA                         CTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
genomic: CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAAgtatgtcttt ... ttccatacagCTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
EST: gi|193540955|gb|FK496089.1|FK496089
EST:     CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA                         CTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
genomic: CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAAgtatgtcttt ... ttccatacagCTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
EST: gi|19453486|gb|BM954896.1|BM954896
EST:     CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA                         CTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
genomic: CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAAgtatgtcttt ... ttccatacagCTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
EST: gi|19453554|gb|BM954964.1|BM954964
EST:     CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAA                         CTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
genomic: CCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAAgtatgtcttt ... ttccatacagCTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
EST: gi|14011684|gb|BG726606.1|BG726606
EST:     CTGGTTTCATCTGGTGCTGATGCTCAA                         CTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA
genomic: CTGGTTTCATCTGGTGCTGATGCTCAAgtatgtcttt ... ttccatacagCTTTGTGTATGGAGTATTGATACATGGGAGAAAAGAAAATCAGTTCCTATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAATCTAAATTGAAGGGTCATCAAAAGCGAATTACTGGTTTAGCCTTTTCAACCTGTCTTAACATCCTGGTTTCATCTGGTGCTGATGCTCAAgtatgtcttttaactgttctcctttcattcagggtgattcggaaaacctcatacataataatttcttttggagatctctgttagttatctgtctttggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT