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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtatgtcttcttatgtgttttaagtttaactacttagtatctcatggtgattaatttatattttttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGTTGATCTAGTTTTCAGAAAGGAACTTCCACTGAG

Basic information

species Glycine max
transcript GLYMA16G27210.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27210.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G24170.2 (Arabidopsis thaliana), 3'ss of exon 7
-------------gtgtgtatgtcttcttatgtgttttaagt-ttaactactt--agtatctcatggtgattaatttatattttttt-tcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGTTGATCTAGTTTTCAGAAAGGAACTTCCACTGAG
||| | || || ||| | | | | || || | | | || | || | | || |||| | || |||||||| || ||||||||||| ||||||||||| |||||| | || || ||| || | ||||| ||||||||||| || ||
gtaatgtcttcctcaatgttttcctcctgctgtacctaacatgccagctgtttcaatggtttaatcctcgtttctatttacgttttaattagGTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAG
















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|298193865|gb|HO040513.1|HO040513
EST:     GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGG                         TTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
genomic: GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGGgtgtgtatgt ... tttttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
EST: gi|27424557|gb|CA936077.1|CA936077
EST:     GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGG                         TTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
genomic: GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGGgtgtgtatgt ... tttttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
EST: gi|254323260|gb|GR840065.1|GR840065
EST:     GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGG                         TTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
genomic: GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGGgtgtgtatgt ... tttttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
EST: gi|9901924|gb|BE610892.1|BE610892
EST:     GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGG                         TTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
genomic: GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGGgtgtgtatgt ... tttttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
EST: gi|151394106|gb|EV263977.1|EV263977
EST:     GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGG                         TTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
genomic: GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGGgtgtgtatgt ... tttttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
EST: gi|208083700|gb|GD881704.1|GD881704
EST:     GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGG                         TTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
genomic: GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGGgtgtgtatgt ... tttttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
EST: gi|8670051|gb|BE191158.1|BE191158
EST:     GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGG                         TTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
genomic: GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGGgtgtgtatgt ... tttttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
EST: gi|193492241|gb|FK455267.1|FK455267
EST:     GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGG                         TTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT
genomic: GCACTAAGTTTAGAGGATCTTCCAAAACATGCTGTGGTTCTTGGAGGAGGgtgtgtatgt ... tttttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttaagtttaactacttagtatctcatggtgattaatttatattttttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGTTGATCTAGTTTTCAGAAAGGAACTTCCACTGAG
                                gattaat  putative branch site (score: 3)
 tttatattttttttc  CT-rich tract
 tcatggtgattaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtatgtcttcttatgtgttttaagtttaactacttagtatctcatggtgattaatttatattttttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGTTGATCTAGTTTTCAGAAAGGAACTTCCACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA