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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAAGTTAGGGTTTTTGGGGGTGAAGTTGCGCTTCCGGCACTTCCACTTCCACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtctttctcttcatttctttttcttttcttaaaaaaattccaagttttgatacactccgtcggtattaatatgcaattgtctgttctttttgggaatgcggcag

Basic information

species Glycine max
transcript GLYMA11G09150.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S475_6V6.3 (Physcomitrella patens), 5'ss of exon 1
TTAAGTTAGGGTTTTTGGGGGTGAAGTTGCGCTTCCGGCACTTCCACTTCCACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagt----------ctttctcttcatttctttttcttttcttaaaaaaatt---ccaagttttgatacactc---cgtcggtattaatatgcaattgtc-tgttctttttgggaatgcggcag
| || || | || | | | || | | | |||||||||||| ||||| ||||| ||||||||||||||||| | || | | | ||| |||| | || || | | | | | | || | || || | | ||||| | | || || || | |
---------------------TTCAGGTGGGTTTGTAGTAAT--CAGGGTCGGCTGTCATTCACCATGAGCAAATCAGGGCAACCCCCGGATTTGAAGAAGTACATGGACAAGAAGCTGAACAgtaagacatgtttattttttggaaggcgtttttctaccatctcctctattcatacttctgttgcgagaggcaatcaaaataattttcctgtgactactaa--

upper sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S475_6V6.2 (Physcomitrella patens), 5'ss of exon 2
TTAAGTTAGGGTTTTTGGGGGTGAAGTTGCGCTTCCGGCACTTCCACTTCCACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagt----------ctttctcttcatttctttttcttttcttaaaaaaatt---ccaagttttgatacactc---cgtcggtattaatatgcaattgtc-tgttctttttgggaatgcggcag
|| | || | | | || | | | |||||||||||| ||||| ||||| ||||||||||||||||| | || | | | ||| |||| | || || | | | | | | || | || || | | ||||| | | || || || | |
--------------------------GTGGGTTTGTAGTAAT--CAGGGTCGGCTGTCATTCACCATGAGCAAATCAGGGCAACCCCCGGATTTGAAGAAGTACATGGACAAGAAGCTGAACAgtaagacatgtttattttttggaaggcgtttttctaccatctcctctattcatacttctgttgcgagaggcaatcaaaataattttcctgtgactactaa--

upper sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S475_6V6.1 (Physcomitrella patens), 5'ss of exon 2
TTAAGTTAGGGTTTTTGGGGGTGAAGTTGCGCTTCCGGCACTTCCACTTCCACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagt----------ctttctcttcatttctttttcttttcttaaaaaaatt---ccaagttttgatacactc---cgtcggtattaatatgcaattgtc-tgttctttttgggaatgcggcag
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----------------------------------------TAATCAGGGTCGGCTGTCATTCACCATGAGCAAATCAGGGCAACCCCCGGATTTGAAGAAGTACATGGACAAGAAGCTGAACAgtaagacatgtttattttttggaaggcgtttttctaccatctcctctattcatacttctgttgcgagaggcaatcaaaataattttcctgtgactactaa--

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|18730335|gb|BM525820.1|BM525820
EST:     TCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: TCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|31561892|gb|CD487730.1|CD487730
EST:     CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|254346216|gb|GR859829.1|GR859829
EST:     CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|298176503|gb|HO026738.1|HO026738
EST:     CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|151398942|gb|EV268813.1|EV268813
EST:     CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|192327127|gb|FK015519.1|FK015519
EST:     CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|31467429|gb|CD409457.1|CD409457
EST:     CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|31306974|gb|CD392177.1|CD392177
EST:     CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|151412914|gb|EV282726.1|EV282726
EST:     CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|19452429|gb|BM953839.1|BM953839
EST:     GCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: GCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|33388212|gb|CA851419.1|CA851419
EST:     ACTTCTTCATCACCATGAGCAGGTCAGGNCAACCACCGGNATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: ACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGG-ATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|6667111|gb|AW278570.1|AW278570
EST:     CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|193327961|gb|FK295550.1|FK295550
EST:     ACTTCTTCATCACCATGAGCAGGTCAGGCCAACCTACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: ACTTCTTCATCACCATGAGCAGGTCAGGCCAACC-ACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA
EST: gi|151410461|gb|EV280276.1|EV280276
EST:     CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAA                         GTACATGGACAAGAAGCTTCAGA
genomic: CACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtcttt ... aatgcggcagGTACATGGACAAGAAGCTTCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAAGTTAGGGTTTTTGGGGGTGAAGTTGCGCTTCCGGCACTTCCACTTCCACTTCTTCATCACCATGAGCAGGTCAGGCCAACCACCGGATTTGAAGAAgtaagtctttctcttcatttctttttcttttcttaaaaaaattccaagttttgatacactccgtcggtattaatatgcaattgtctgttctttttgggaatgcggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA