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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacacaaacactttttgttttatgtttcacaaaatcatgggcaatcgccaatttcgtgtctttcttcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAGAGAGCGTATTTTGAGTCACTGGCACTGAAAGAAGAGGGTCGTTTGAGCC

Basic information

species Glycine max
transcript GLYMA10G40730.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G40730.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0091g00100.t01 (Vitis vinifera), 3'ss of exon 1
--------------gtaacacacaaacactttttgttttatgtttcacaaa----atcatgggcaatcgccaatttcgtgtctttcttctta---tatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAGAGAGCGTATTTTGAGTCACTGGCACTGAAAGAAGAGGGTCGTTTGAGCC
                 | ||| | | |  | || |   |  ||  | |||    |  |||    | |     |    |||  || |  | |   |  ||||  |||| ||| | ||| | ||||||||||||||||| |||||||||||  | |||||||||||  |   |||  ||| |||  || |||| | | || 
catatctagaatattctatacaaatatagctgttataacagattaaataaatgctagtatgctagaactgttgtaagatgtggttgtgttgagagtgcagGCGTTGCCGTACATACGTAGTATAGGGGAATCGTGGCCGATGACGAAGGACCGGGCGTATTTTGAAGCGACGGCTTTGAGAGAGCAGCGTCGCTGGTGCT

upper sequence: GLYMA10G40730.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0091g00080.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------------gtaacacacaaacactttttg------tttta--tgtttcacaaaatcatgggcaatcgccaatttcg---tgtctttcttctta---tatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAGAGAGCGTATTTTGAGTCACTGGCACTGAAAGAAGAGGGTCGTTTGAGCC
                                                   || | |      |  | ||      |||||  || ||   ||  | | |   ||  | |  ||      |||  || |  | |   |  ||||  |||| ||| | ||||| ||||||||||||||||| |||||||||||  | |||||||||||  |   |||| ||| |||  || |||| | | || 
gtacaaattttgattcataacggcacctcacaaattcagattcttactgaaaaaaaatggcttcactgtggaagaattttaagtgcttgtgaaggttaggtcaaagtgactgttgtaagatgtggttgtgttgagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAACGGGCGTATTTTGAAGCGACGGCATTGAGAGAGCAGCGTCGCTGGTGCT
















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|16347795|gb|BI973390.1|BI973390
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacacaca ... tcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|192297825|gb|FG988323.1|FG988323
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacacaca ... tcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|298187248|gb|HO034397.1|HO034397
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacacaca ... tcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|192295492|gb|FG987106.1|FG987106
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacacaca ... tcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|209714541|gb|BW684890.1|BW684890
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacacaca ... tcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|207734310|gb|GD711602.1|GD711602
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAGACAG                         GCTCTGCCATACG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacacaca ... tcttatatagGCTCTGCCATACG
EST: gi|13312051|gb|BG405694.1|BG405694
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacacaca ... tcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|16347840|gb|BI973435.1|BI973435
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacacaca ... tcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|213587037|gb|DB965867.1|DB965867
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacacaca ... tcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|14259084|gb|BG881992.1|BG881992
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacacaca ... tcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|7926168|gb|AW832194.1|AW832194
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacacaca ... tcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtttcacaaaatcatgggcaatcgccaatttcgtgtctttcttcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAGAGAGCGTATTTTGAGTCACTGGCACTGAAAGAAGAGGGTCGTTTGAGCC
                               tttcgtgtctttcttc  CT-rich tract
                                        tttcttcttatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacacacaaacactttttgttttatgtttcacaaaatcatgggcaatcgccaatttcgtgtctttcttcttatatagGCTCTGCCATACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAGAGAGCGTATTTTGAGTCACTGGCACTGAAAGAAGAGGGTCGTTTGAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG