Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgacattatgtatttgtattcttagtctcgatgttagatcgaaatggctaatgaactcatgtctattctcatgggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAGGGGCAGTTGATTTTCTTATAAAACCCATTCGGAAGAATGAGCTTAGGAA

Basic information

species Glycine max
transcript GLYMA07G05530.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05530.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0048g02540.t01 (Vitis vinifera), 3'ss of exon 2
------------gtatgttgacattatgtatttgtattcttagtctcgatgtt--agatcgaaatgg---ctaatgaactcatg-tctattctcatgggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAGGGGCAGTTGATTTTCTTATAAAACCCATTCGGAAGAATGAGCTTAGGAA
            |  ||||    || |||  |  | | |  ||| | | | ||  ||||   | | |   ||||  || | ||  | | ||||||||    ||||||||||||||||||||||||  |||||||||  |||||||||||||| |||||||| | ||| |||||| | || ||  || ||||||||||||| |||||
gtatgtgatcttgagtgttt-tgttttgtgatcttttccacagttttggtcttttagatgagagttgaacctaaacaagttataatttcttctcatgatcatgcagTGATGTCTTCTCATGATTCAATTAGCATGGTTTTGAAATGCATGTTGAAAGGGGCCGCTGACTTTCTTGTCAAGCCTGTTAGGAAGAATGAGCTGAGGAA
















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|18041234|gb|BM309528.1|BM309528
EST:     TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTCCAGTCATAA                         TGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
genomic: TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTCCAGTCATAAgtatgttgac ... gggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
EST: gi|208323744|gb|GE122315.1|GE122315
EST:     ATTTAGTAAAAACATTCCAGTCATAA                         TGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
genomic: ATTT-GTAAAAACATTCCAGTCATAAgtatgttgac ... gggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
EST: gi|213595702|gb|DB962474.1|DB962474
EST:     TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTCCAGTCATAA                         TGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
genomic: TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTCCAGTCATAAgtatgttgac ... gggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
EST: gi|208332607|gb|GE130272.1|GE130272
EST:     GTAAAAACATTCCAGTCATAA                         TGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
genomic: GTAAAAACATTCCAGTCATAAgtatgttgac ... gggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
EST: gi|209726010|gb|BW654795.1|BW654795
EST:     TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTCCAGTCATAA                         TGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
genomic: TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTCCAGTCATAAgtatgttgac ... gggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
EST: gi|193371412|gb|FK336925.1|FK336925
EST:     TTTGT-AAAACATTCCAGTCATAA                         TGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
genomic: TTTGTAAAAACATTCCAGTCATAAgtatgttgac ... gggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
EST: gi|208269240|gb|GE070248.1|GE070248
EST:     TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTTCAGTCATAA                         TGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
genomic: TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTCCAGTCATAAgtatgttgac ... gggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
EST: gi|208167545|gb|GD965169.1|GD965169
EST:     AACATTCCAGTCATAA                         TGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
genomic: AACATTCCAGTCATAAgtatgttgac ... gggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
EST: gi|208187444|gb|GD985474.1|GD985474
EST:     AAACATTCCAGTCATAA                         TGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
genomic: AAACATTCCAGTCATAAgtatgttgac ... gggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
EST: gi|207818832|gb|GD790303.1|GD790303
EST:     TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTCCAGTCATAA                         TGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
genomic: TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTCCAGTCATAAgtatgttgac ... gggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAG
EST: gi|208029283|gb|GD830135.1|GD830135
EST:     TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTCCAGTCATAA                         TGATGTCTTCTCATGATTCG
genomic: TCTTTCTTTGATCATGGAGCATGACATTTGTAAAAACATTCCAGTCATAAgtatgttgac ... gggtgtgcagTGATGTCTTCTCATGATTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgatgttagatcgaaatggctaatgaactcatgtctattctcatgggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAGGGGCAGTTGATTTTCTTATAAAACCCATTCGGAAGAATGAGCTTAGGAA
                  ggctaat  putative branch site (score: 3)
                     taatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgacattatgtatttgtattcttagtctcgatgttagatcgaaatggctaatgaactcatgtctattctcatgggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAGGGGCAGTTGATTTTCTTATAAAACCCATTCGGAAGAATGAGCTTAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT