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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattacctgtcttacctgccctctgttttccttccctcactccattctagctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA

Basic information

species Glycine max
transcript GLYMA15G07790.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g56300.1 (Oryza sativa), 3'ss of exon 6
----------------------gtgaattacctgtcttacctgccctctgttttccttccctcactccattctagctctcttatttgttaaa-----tctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA
                       |||      ||  |||           ||| |   | ||   ||   | |    ||||  | || | ||     | || ||| ||||||||||| |||||||| ||||| |||||||| || || ||||| || || ||||||||||| || ||||| || || |||||||| |||||||| 
gtaatcccgtggctggctttctttgatccgtgtgaattattgaaaaatgatttactgcctcttcatctgctgttaagctctgttgtgatgaactcctttttgcagATATGATATTGATATGACCAAATGCATCTATTGTGGCTTCTGCCAAGAAGCTTGTCCTGTTGATGCCATCGTTGAGGGTCCTAACTTTGAGTTTGCTACT

upper sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G072806_T01 (Zea mays), 3'ss of exon 6
--------------------------------gtgaattacctgtcttacctgccctctgttttccttccctca-ctccattctag--ctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA
                                || |||      | | |  | ||| |||| |||      | | ||  | |||     ||| ||  || |     ||  |||||||||||||||||||||||| |||||||| ||||| || || |||||||| ||||| || ||||| |||||||| ||||| |||||||| |||||||| 
gtaatcaaaatgaaggtttttctctcttttttgtcaatagaac-tatgatttacccactgtgttctgcaattaaactttaatctgaatttctgttgcttttatctcctcacagGTATGATATTGACATGACCAAATGCATTTACTGTGGGTTCTGCCAAGAGGCTTGCCCAGTCGATGCTATTGTTGAGGGGCCTAACTTTGAGTTTGCTACT

upper sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
lower sequence: AC195340.3_FGT002 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------------gtgaattacctgtcttacctgccctctgttttccttccctc--actccattct--agctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA
                                                                               ||| |         |   ||   | |||| |  | |  |   ||| ||||||  |  | | ||  || ||     |  ||| |||||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| || ||||| |||||||| ||||| |||||||| ||||| || 
gtaatcaaaatgaagtttttcctctttcttttttggacttgtggctgatatcgggtttcaactcgagtctacctcaacttgattgggacaaagtctttgttgt-tgttcttatgcaattaaacttcattctgaacttgtgttgcttttttctcatcacagATATGATATTGACATGACCAAATGCATTTACTGTGGGTTCTGTCAAGAGGCTTGCCCAGTCGATGCTATTGTTGAGGGGCCTAACTTTGAGTTTGCCACT

upper sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G79010.1 (Arabidopsis thaliana), 3'ss of exon 6
---gtgaattacctg--tcttacctgccctctgttttccttccctcactccattctagctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA
    | |      |   ||| |  |  |  |  | | | |||  | | | |  | |     |  | |  | |  ||| | |||||| ||||| |||||||| || ||||| || ||||| || || ||||| || ||||| |||||||| || |||||||| || ||||||||||| || || 
gtcatcatccctttagttctcatttatcaaccatctgctttct-ttattaccctttcatgatgatttgagctgtatcgtacagGTACGATATCGACATGACAAAATGCATCTACTGTGGTTTCTGCCAAGAAGCTTGCCCCGTTGATGCAATCGTTGAAGGACCTAACTTTGAATTCGCAACC

upper sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G16700.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------------gtgaattacctg-tcttacctgccctctgttttccttccct-cactccattctagctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA
                                  |  ||||  |  |  |  ||   |||| |  | ||||  |  | | | |  |       || || |   |    | |||||||||||| |||||||| || ||||| |||||||| || || ||||| || |||||||||||||| || || ||||| ||||||||||| ||||| || 
gtcaccctctaagttcccgtttattaaccatatatatattatttaatactgtcttgtctctatggttcttctatatatttcgtagtgtagtgattgttcg--gagctgtacagGTATGATATCGACATGACGAAATGCATCTATTGTGGTTTCTGCCAAGAAGCTTGCCCTGTTGATGCAATCGTGGAAGGACCAAACTTTGAGTTTGCAACC

upper sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0063g02550.t01 (Vitis vinifera), 3'ss of exon 6
gtgaattacctgtcttacctgccctctgttttccttccctcactccatt-ctagctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA
||||     ||  |||   ||  |||| | | |  || |||||||  |  ||  ||| ||  || ||| ||  |  |||||| || ||||||||||||||||||||||| |||||||| || ||||||||||||||||||||||| ||||| ||||| || |||||||||||  |||||
gtgatgggtcttacttgg-tgatctctatct-cactcactcactcactagctcactcactagttggtttaacttcacagGTACGACATTGACATGACCAAGTGCATTTACTGTGGATTCTGCCAAGAGGCATGCCCTGTTGATGCCATTGTGGAAGGTCCCAACTTTGAATTCACTACA

upper sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
lower sequence: EDO96988 (Chlamydomonas reinhardtii), 3'ss of exon 5
---------------------gtgaattacctgtcttacctgccctctgttttccttccctcactccattctagctctcttatttgttaaatcttt-cagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA
                     |      ||  |  |    |||     ||  || | |  ||          |   |      ||  |   ||    |||||| || ||||||||||||||||||||||| || || || || || ||||| ||||| || || ||||| || || || || ||||| || ||  |||| 
gccatgcggtgacactgctgcgcagtcgacacgattctggtgcaaaacgtcatcgtgctgtccggttggctgactgcatgcccttcatgtgtcgccgcagGTACGACATTGACATGACCAAGTGCATTTACTGCGGCTTCTGCCAGGAGGCCTGCCCCGTGGACGCGATCGTGGAGGGCCCCAACTTCGAGTTCTCTACC

upper sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------gtgaattacctgtct-tacctgccctctgttttccttccctcactccattctagctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA
                         | |    | |||  | ||| |   || |||     | |        ||||  | | ||  |   |  || || ||| ||||||||||||||||| || ||||| || || || ||||| ||||| || |||||||| || || ||||| ||||| || |||||||| ||  | || 
acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgtaggcgagctctaagtttatt-ctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG

upper sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
lower sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
gtgaattacctgtcttacctgccctctgttttccttccctcactccattctagctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA
               |||      | ||||||| ||   |   |    |       |   |    ||     |  |||||||||||| || ||||| |||||||| || || ||||| || |||||||| ||||| || ||||| || ||||| || ||||| ||||| ||||| || 
------------gtatactaagtttgtgttttcttttggttggtttgatagtaacttagcaccctttg----tcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC

upper sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
lower sequence: EFJ15239 (Selaginella moellendorffii), 3'ss of exon 5
gtgaattacctgtcttacctgccctctgttttccttccctcactccattctagctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA
           || |     |     | |||   ||  ||   |  ||  || || |   |    ||     |  |||||||||||| || ||||| |||||||| || || ||||| || |||||||| ||||| || ||||| || ||||| || ||||| ||||| ||||| || 
-----------gtatactaagtttgttttttcttttggctggtttgatagtaact-tagcaccctttg----tcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC

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|57574474|gb|CX547449.1|CX547449
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|57574779|gb|CX547754.1|CX547754
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|209720061|gb|BW651117.1|BW651117
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|298183653|gb|HO028866.1|HO028866
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTT
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTT
EST: gi|22522900|gb|BU081711.1|BU081711
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|151408171|gb|EV277979.1|EV277979
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|213613738|gb|DB961235.1|DB961235
EST:     ATCACAATTGAGGCTGGGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|213595771|gb|DB966214.1|DB966214
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|192308816|gb|FG999813.1|FG999813
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|151400277|gb|EV270091.1|EV270091
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|213616933|gb|DB959245.1|DB959245
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGCAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|209728235|gb|BW651670.1|BW651670
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|151395722|gb|EV265599.1|EV265599
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|298187849|gb|HO031806.1|HO031806
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|192308815|gb|FG999812.1|FG999812
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|213615400|gb|DB965500.1|DB965500
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|209701814|gb|BW683146.1|BW683146
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATT-ATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|298189184|gb|HO037587.1|HO037587
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTG
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTG
EST: gi|58020317|gb|CX707059.1|CX707059
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
EST: gi|58016737|gb|CX703479.1|CX703479
EST:     ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCG                         GTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC
genomic: ATCACAATTGAGGCTGAGGAGCGAGAAGATGGAAGCCGCAGGACAACTCGgtgaattacc ... aatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgttttccttccctcactccattctagctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA
             ccctcac  putative branch site (score: 3)
                                               tctttc  putative PPT
                                   ttatttgttaaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattacctgtcttacctgccctctgttttccttccctcactccattctagctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG