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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaattggtacaagttgttacttgctaggtccacagcaccacagtggttgttgagtgttttttcttctatcatgctcaactctgaatctctgattgcagGTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACATGATCCACGAATTGATCCATTTGATTAGAG

Basic information

species Glycine max
transcript GLYMA12G00600.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G00600.3 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g43500.1 (Oryza sativa), 3'ss of exon 7
ataaattgg---tacaagttgttacttgctaggtccacagcaccacagtggttgttgagtgttttttctt-ctatcatgct--------caactctgaatct-------ctgattgcagGTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACATGATCCACGAATTGATCCATTTGATTAGAG--------------------
 |||||  |   |        | | |  | |   | |   ||    | |  |    |  | |||   ||| ||||  ||          || | |||| |          || |||||||| ||||||||||||||||| ||||| || ||||| |||||||| || || || || ||||||||||| |||||||| |                     
gtaaatcagccttttgcacaatgattcccaacaacaatgtcattcaaataatatacgcatatttccacttgctattttggattgaaaaacagccctgatttcaaacaaaatgtttgcagGTGATGTGTCCAACATGTCTCTGCACGGGGATGGCAATGGCAAGTGAGCACGACCCTCGAATTGATCCGTTTGATTAAAATGCACGTCATAGTTCAGAAA

upper sequence: GLYMA12G00600.3 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0013g00350.t01 (Vitis vinifera), 3'ss of exon 6
ataaattggtacaagttgttacttgctaggtccacagcaccacagtggttgttgagtgttttttcttctatcatgctcaactctgaatctctgatt-gcagGTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACATGATCCACGAATTGATCCATTTGATTAGAG--------------------
 | |  |  | | ||| |     || ||   ||  ||  | ||| ||    || ||   |||    | | | |        |     | |||  || |||||| ||||| || ||||| || || ||||| ||||  ||||| ||||| |||||||||||||| ||||| ||||| |||||                    
-tcacctccttctagtgggggtatgatacaacccaagttcaacactgaaacttcagaaatttccagtttgtgaactagggataaatttatctattttgcagGTCATGTGCCCCACATGCCTCTGTACTGGGATGGAAATGGCGAGCGAGCATGATCCACGAATAGATCCCTTTGACTAGAGTTGCATCATTTCCTTCATAC

upper sequence: GLYMA12G00600.3 (Glycine max), 3'ss of exon 7
lower sequence: PP1S237_60V6.2 (Physcomitrella patens), 3'ss of exon 8
ataaattggtacaagttgttacttgctaggtccacagcaccacagtggttgttgagtgttttttcttctatcatgctcaactctgaatc---tctgattgcagGTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACATGATCCACGAATTGATCCATTTGATTAGAG
 | |   ||| |||    |||| |  |       ||  |  | ||   | |||   | | |||| |    || |     ||   ||||         |||||||| ||||||||||||||||| ||||| || |||||  |||| || ||||| ||||| || ||||| || ||  |      
gttacacggttcaaagc-ttacgttatcaaagggcaatat-atagccttagtttc-tttcttttatgtagtcgttgctgaccgggaattgaacacacttgcagGTGATGTGTCCAACATGTCTCTGCACAGGCATGGCACTGGCTAGTGAACACGATCCTCGCATTGACCCTTTCCA------

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|192307758|gb|FK001702.1|FK001702
EST:     TTTCACCACCAAAAACTGAGAGATGTTCAAATTGCTCTGGATCTGGCAAG                         GTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACAT
genomic: TTTCACCACCAAAAACTGAGAGATGTTCAAATTGCTCTGGATCTGGCAAGgtcggttatt ... ctgattgcagGTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACAT
EST: gi|22525484|gb|BU084295.1|BU084295
EST:     TTTCACCACCAAAAACTGAGAGATGTTCAAATTGCTCTGGATCTGGCAAG                         GTTATGTGTCCAACATGTCTTTGCACTGGAA
genomic: TTTCACCACCAAAAACTGAGAGATGTTCAAATTGCTCTGGATCTGGCAAGgtcggttatt ... ctgattgcagGTTATGTGTCCAACATGTCTTTGCACTGGAA
EST: gi|208189309|gb|GD985645.1|GD985645
EST:     TTTCACCACCAAAAACTGAGAGATGTTCAAATTGCTCTGGATCTGGCAAG                         GTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACAT
genomic: TTTCACCACCAAAAACTGAGAGATGTTCAAATTGCTCTGGATCTGGCAAGgtcggttatt ... ctgattgcagGTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACAT
EST: gi|207827337|gb|GD799132.1|GD799132
EST:     TTTCACCACCAAAAACTGAGAGATGTTCAAATTGCTCTGGATCTGGCAAG                         GTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAA
genomic: TTTCACCACCAAAAACTGAGAGATGTTCAAATTGCTCTGGATCTGGCAAGgtcggttatt ... ctgattgcagGTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAA
EST: gi|120491318|gb|EH219485.1|EH219485
EST:     TTTCACCACCAAAAACTGAGAGATGTTCAAATTGCTCTGGATCTGGCAAG                         GTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACAT
genomic: TTTCACCACCAAAAACTGAGAGATGTTCAAATTGCTCTGGATCTGGCAAGgtcggttatt ... ctgattgcagGTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttgttgagtgttttttcttctatcatgctcaactctgaatctctgattgcagGTTATGTGTCCAACATGTCTTTGCACTGGAATGGCCATGGCAAGCGAACATGATCCACGAATTGATCCATTTGATTAGAG
                                           ctctgat  putative branch site (score: 4)
                                          tctct  CT-rich tract
             ttttttctt  TA-rich tract