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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttactttccttttcttctcctttcatctccctttgttgaagtgtgaagatggattagtggaaaatagcaatgtattttgtttacaaattattcagtccaaatacattgccattttcacctaccctttttaactacaactgagaacacctgtccttttgactttgtttatgtttgtcatcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG

Basic information

species Glycine max
transcript GLYMA09G39150.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 12
gttactttccttttcttctcctttcatctccctttgttgaagtgtgaagatggattagtggaaaatagcaatgtattttgtttacaaattattcagtccaaatacattgccattttcacctaccctttttaactacaactgagaacacctgtccttttgactttgtttatgtttgtcatcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG
                                                                                        | ||||  | | |      | | | ||||  || |  ||   |  |  ||   |||     | || |||  |||   || |  |   |||   | |  ||||||||| |||||||||||| |||||||||||  ||    | || |  |  ||||| |||||||||
---------------------------------------------------------------------------------------gtcattc--ttctatctggctccaagtttc--ctgctattgacagttttaa---aga-----tttcgtttgcactcacttcaattgattcaatttct--agGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCCCTTGTTAAACTACAG

upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G422539_T01 (Zea mays), 3'ss of exon 3
gttactttccttttcttctcctttcatctccctttgttgaagtgtgaagatggattagtggaaaatagcaatgtattttgtttacaaattattcagtccaaatacattgccattttcacctaccctttttaactacaactgagaacacctgtccttttgactttgtttatgtttgtcatcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG
                                                                                            ||| ||    |  ||   | | |     | |  || |||||      | |  |     ||     | ||||   ||   ||| |          ||||||||| |||||||||||| |||||||||||  ||    | || |  |  ||||| |||||||||
-------------------------------------------------------------------------------------------gtcattct---tctatctgcctctggttttgctgttattaacagtttttaaagattttcgttgcactcacttaaattcaatttct----------agGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCGGCCCTTGTTAAACTACAG

upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G481395_T01 (Zea mays), 3'ss of exon 3
gttactttccttttcttctcctttcatctccctttgttgaagtgtgaagatggattagtggaaaatagcaatgtattttgtttacaaattattcagtccaaatacattgccattttc--acctaccctt--tttaactacaactgagaacacctgtcc-ttttgactttgtttatgtttgtcatcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG----
                                                                                                            | |||| |   | || ||  |  |||  ||   | | | |     |     |||||  |    | |  |   |     | |  ||||||||| |||||||||||| |||||||||||  ||    | || |  |  ||||| |||||| ||    
------------------------------------------------------------------------------------------------------------gtcattcttctatctgcctctggttttgctgttattaacagtttttaaagattttggttgcactcacttaaattcaatt-tctagGCTGATGCCTTTGCCAAGAACCTTGGATATGC-CCTCAGCTCCGAGCGGCCCTTGTTAAACTATAGGTAA

upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G305559_T01 (Zea mays), 3'ss of exon 3
gttactttccttttcttctcctttcatctccctttgttgaagtgtgaagatggattagtggaaaatagcaatgtattttgtttacaaattattcagtccaaatacattgccattttc--acctaccctt--tttaactacaactgagaacacctgtcc-ttttgactttgtttatgtttgtcatcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG
                                                                                                            | |||| |   | || ||  |  |||  ||   | | | |     |     |||||  |    | |  |   |     | |  ||||||||| |||||||||||| |||||||||||  ||    | || |  |  ||||| |||||||||
------------------------------------------------------------------------------------------------------------gtcattcttctatctgcctctggttttgctgttattaacagtttttaaagattttggttgcactcacttaaattcaatt-tctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCGGCCCTTGTTAAACTACAG

upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G702159_T01 (Zea mays), 3'ss of exon 13
gttactttccttttcttctcctttcatctccctttgttgaagtgtgaagatggattagtggaaaatagcaatgtattttgtttacaaattattcagtccaaatacattgccattttcacctaccctttttaactacaactgagaacacctgtcc-ttttgactttgtttatgtttgtcatcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG
                                                                                                        ||||    | |   ||| |   |||   ||   | | | |     |     |||||  |    | |  |   |   | | |  ||||||||| |||||||||||| |||||||||||  ||    | || |  |  ||||| |||||||| 
------------------------------------------------------------------------------------------------------gtcattcttctatctgcctccgagttt--gctgttattaacagtttttaaagattttggttgcactcacttaaatt-ccatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCGGCCCTTGTTAAACTACAT

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|207818473|gb|GD790728.1|GD790728
EST:     AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG                         GCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
genomic: AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAGgttactttcc ... tcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
EST: gi|192302659|gb|FG994897.1|FG994897
EST:     AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG                         GCTGATGGCTTTGCCAAGAAGCTTGGATATGTATCTGGATTACGCGGTGGT
genomic: AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAGgttactttcc ... tcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
EST: gi|7029492|gb|AW459275.1|AW459275
EST:     AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG                         GCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
genomic: AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAGgttactttcc ... tcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
EST: gi|5175463|gb|AI759796.1|AI759796
EST:     AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG                         GCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
genomic: AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAGgttactttcc ... tcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
EST: gi|7690863|gb|AW759000.1|AW759000
EST:     AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG                         GCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
genomic: AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAGgttactttcc ... tcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
EST: gi|19270564|gb|BM886820.1|BM886820
EST:     AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG                         GCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
genomic: AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAGgttactttcc ... tcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
EST: gi|5175455|gb|AI759788.1|AI759788
EST:     AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG                         GCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
genomic: AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAGgttactttcc ... tcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
EST: gi|214005851|gb|DB988692.1|DB988692
EST:     TCT-ATCAGCTTTGCG-GAGAACCTAGTCAGCCGATCATTTGAATTTCAG                         GCTGATGGCTTTGCCAAGAAGCTTTGATATGCATCTGGATTACGCGGTGTT
genomic: T-TGGTCAGCTTTG-GTCTGAACCTAGTCAGCCGATCATTTGAATTTCAGgttactttcc ... tcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT
EST: gi|22933929|gb|BU551068.1|BU551068
EST:     AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG                         GCTGATGGCTTTGCCAAGAAGCNNNGATATGCATCTGGATTACGCGGTGGT
genomic: AATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAGgttactttcc ... tcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaactgagaacacctgtccttttgactttgtttatgtttgtcatcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG
                     ttttgac  putative branch site (score: 3)
                                          tcatcct  putative PPT
                            tttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttactttccttttcttctcctttcatctccctttgttgaagtgtgaagatggattagtggaaaatagcaatgtattttgtttacaaattattcagtccaaatacattgccattttcacctaccctttttaactacaactgagaacacctgtccttttgactttgtttatgtttgtcatcctatgcagGCTGATGGCTTTGCCAAGAAGCTTGGATATGCATCTGGATTACGCGGTGGTCTTGTGAAACTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC