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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctattggatttgatcatttgaggaatgaaaatttatatttacattaagcatgtaaggttcattcttcttcttaccatctaggtccttgattttttttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACTGGAGGTGCAATATCAGCAAAAG

Basic information

species Glycine max
transcript GLYMA12G01980.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G01980.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g07140.t01 (Vitis vinifera), 3'ss of exon 2
gtctattggatttgatcatttgaggaatgaaaatttatatttacattaagcatgtaaggttcattcttcttcttaccatctaggtccttgattttttttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACTGGAGGTGCAATATCAGCAAAAG
||   ||  |    ||     |   |||  | |||| |||     | |  |||||  |    ||| |||    |     |||  |   |  | |||  |   |||| || ||||||||||| | ||||||||| |||||||| || ||||  ||||| |||||||||||||||||||
gtactttaaaaagtatatcaagtcaaattgatatttctataactttcatccatgtttga---attattcactatggggactaattgtgtcgtgtttggtgtaagGCGCGTGCAAAACATGATACAACAAATACAGTTGTTGCGGGGTGTGTTACTGGGGGTGCAATATCAGCAAAAG
















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|298194880|gb|HO043352.1|HO043352
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTCGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tttttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|8827607|gb|BE211337.1|BE211337
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAT                         GCTCGAGCAAAACATGACATAACACATACCAGT-GATGCTGGATGTGCAAC
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tttttcacagGCTCGAGCAAAACATGACATAACAAATACC-GTTGTTGCTGGATGTGCAAC
EST: gi|193546511|gb|FK500952.1|FK500952
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tttttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|20815053|gb|BQ299531.1|BQ299531
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GGTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tttttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|23050120|gb|BU576971.1|BU576971
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tttttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|192296561|gb|FG989133.1|FG989133
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tttttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|8827606|gb|BE211336.1|BE211336
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tttttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|8827246|gb|BE210976.1|BE210976
EST:     NTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tttttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgtaaggttcattcttcttcttaccatctaggtccttgattttttttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACTGGAGGTGCAATATCAGCAAAAG
                                   tccttgattttttttc  CT-rich tract
                                      ttgattttttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctattggatttgatcatttgaggaatgaaaatttatatttacattaagcatgtaaggttcattcttcttcttaccatctaggtccttgattttttttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACTGGAGGTGCAATATCAGCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG