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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTGGTCCCTATCCTGCTGCTCAGGTTGTGAGAGACTTCCAAGGCAAATTTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttattctcttttcaaaatttccatgtcatatttgtgaatggttttcttctctaacctggcatacatatcctgatcttttacag

Basic information

species Glycine max
transcript GLYMA10G38840.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G38840.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0020g04160.t01 (Vitis vinifera), 5'ss of exon 2
TCGTGGTCCCTATCCTGCTGCTCAGGTTGTGAGAGACTTCCAAGGCAAATTTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttattctcttttcaa--aatttccatgtcatatttgtgaatggttttcttctctaacctggcatacatatcctgatcttttacag-------------------------------------------
| | ||||| |||||||| | ||| |||||||||||  |||| || |||||||||||| |||| ||||||||   |   |  ||||||||| | ||||| |||||| |  || ||  | |  |||||   | ||  ||||   | |     |||| | |   ||   ||   |||  | | ||| |                                               
TAGAGGTCCATATCCTGCAGATCAAGTTGTGAGAGATCTCCATGGGAAATTTGCATTTGTTCTCTATGACAGCTCTAACAGAACTGCATTTCTAGCTGCTgtgagtaaaccttttggccagtaattttgctatccaattt-caagtatccctcttgt-tgctctcagattgttatgatcaccttctttgaaggcagcttacatcaggtgtaactttacccacatgtaatgcag

upper sequence: GLYMA10G38840.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0036g00050.t01 (Vitis vinifera), 5'ss of exon 3
TCGTGGTCCCTATCCTGCTGCTCAGGTTGTGAGAGACTTCCAAGGCAAATTTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttattctcttttcaa--aatttccatgtcatatttgtgaatggttttcttctctaacctggcatacatatcctgatcttttacag-------------------------------------------
| | ||||| |||||||| | ||| |||||||||||  |||| || |||||||||||| |||| ||||||||   |   |  ||||||||| | ||||| |||||| |  || ||  | |  |||||   | ||  ||||   | |     |||| | |   ||   ||   |||  | | ||| |                                               
TAGAGGTCCATATCCTGCAGATCAAGTTGTGAGAGATCTCCATGGGAAATTTGCATTTGTTCTCTATGACAGCTCTAACAGAACTGCATTTCTAGCTGCTgtgagtaaaccttttggctagtaattttgctatccaattt-caagtatccctcttgt-tgctctcagattgttatgatcaccttctttgaaggcagcttacatcaggtgtaactttacccacatgtaatgcag
















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|10237547|gb|BE806435.1|BE806435
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|254326314|gb|GR840906.1|GR840906
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|192295822|gb|FG990874.1|FG990874
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|7283825|gb|AW596427.1|AW596427
EST:     TTGCATCTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|192333019|gb|FK024668.1|FK024668
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|4293386|gb|AI442040.1|AI442040
EST:     T-GCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGGTCCCCTTTG-CTGGGGAACTGATGCTGATGGA
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCC-TTTGTCTGGGGAACTGATGCTGATGGA
EST: gi|15814188|gb|BI786463.1|BI786463
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|7283802|gb|AW596404.1|AW596404
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTATGTCTGGGGAACTGATGCTGATGGAGAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|23726996|gb|BU761512.1|BU761512
EST:     AAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: AAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|254320535|gb|GR826984.1|GR826984
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|6667998|gb|AW279449.1|AW279449
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|254326313|gb|GR840905.1|GR840905
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|5606908|gb|AI901006.1|AI901006
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
EST: gi|254320536|gb|GR826985.1|GR826985
EST:     TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCG                         GATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT
genomic: TTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttatt ... tcttttacagGATGCTGATGGGAGTGTTCCCTTTGTCTGGGGAACTGATGCTGATGGAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTGGTCCCTATCCTGCTGCTCAGGTTGTGAGAGACTTCCAAGGCAAATTTGCATTTATTCTGTATGACAGTGGTTCTAAGACTGCATTTGTTGCTGCGgtgagttattctcttttcaaaatttccatgtcatatttgtgaatggttttcttctctaacctggcatacatatcctgatcttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC