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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatgctttataattgtatttaatttaatttataggagcaagcaggaggcaaggatagtggtgataccttctatgttatctttgtttcttcccttctggcagGTTGTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTTGCATGGAATAATTTATGGCTACAGAAGCTCTCTGAGCTTCCAGAAAAAT

Basic information

species Glycine max
transcript GLYMA06G44390.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G44390.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0028g01550.t01 (Vitis vinifera), 3'ss of exon 2
--gtaatatgctttataattgtattt-aatttaattt-------ataggagcaagcaggaggcaaggatagtggtgataccttctatgttatctttgtttcttcccttctggcagGTTGTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTTGCATGGAATAATTTATGGCTACAGAAGCTCTCTGAGCTTCCAGAAAAAT
| | | |||| || || |||| |||||| ||| | | ||| | || | ||| | ||| | || | || ||| | | | || ||||| || ||||||| || ||| | ||||||| ||| ||||| |||||||||||||||| ||| |||||||| ||| |||| ||||||||| | || |
gtatttttttctttttattttcatttcaatttattttttctttcacaatgacaaccctgaaa-agggaaaacccagattctttaaacaataccttaaaat-tcactccctttcagGTCTTATTAAACCAAATAGTGCTTGGTCCATCTGTTGTTGCTATTGTTTTTGCATGGAACAATATATGGCTAGGAAAGTTCTCAGAGCTTCCAAATAAGT
















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|209720744|gb|BW657746.1|BW657746
EST:     GCCTTGACCACTGTCTCCCCAAACCAACAGTCCAGAACCTAGTGTTAAAG                         GTTGTACTAAACCAGATTGTGTTA
genomic: GCCTTGACCACTGTCTCCCCAAACCAACAGTCCAGAACCTAGTGTTAAAGgtaatatgct ... cttctggcagGTTGTACTAAACCAGATTGTGTTA
EST: gi|20207621|gb|BQ133710.1|BQ133710
EST:     GCCTTGACCACTGTCTCCCCAAACCAACAGTCCAGAACCTAGTGTTAAAG                         GTTGTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTT
genomic: GCCTTGACCACTGTCTCCCCAAACCAACAGTCCAGAACCTAGTGTTAAAGgtaatatgct ... cttctggcagGTTGTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTT
EST: gi|23726588|gb|BU761291.1|BU761291
EST:     GCCTTGACCACTGTCTCCCCAAACCAACAGTCCAGAACCTAGTGTTAAAG                         GTTGTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTT
genomic: GCCTTGACCACTGTCTCCCCAAACCAACAGTCCAGAACCTAGTGTTAAAGgtaatatgct ... cttctggcagGTTGTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTT
EST: gi|17023338|gb|BM094372.1|BM094372
EST:     GCCTTGACCACTGTCTCCCCAAACCAACAGTCCAGAACCTAGTGTTAAAG                         GTTGTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTT
genomic: GCCTTGACCACTGTCTCCCCAAACCAACAGTCCAGAACCTAGTGTTAAAGgtaatatgct ... cttctggcagGTTGTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaaggatagtggtgataccttctatgttatctttgtttcttcccttctggcagGTTGTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTTGCATGGAATAATTTATGGCTACAGAAGCTCTCTGAGCTTCCAGAAAAAT
                   ccttctatgttatctt  CT-rich tract
 tatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatgctttataattgtatttaatttaatttataggagcaagcaggaggcaaggatagtggtgataccttctatgttatctttgtttcttcccttctggcagGTTGTACTAAACCAGATTGTGTTAGGTCCATGTGTCATTGCTGTTGTTTTTGCATGGAATAATTTATGGCTACAGAAGCTCTCTGAGCTTCCAGAAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT