Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGCTGAGGATGCCATTGTGAGGCTCACTAGGGAGGTTGTGCCTGGCATGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattctattatctcttgatactcttgtgccacttattcaatttgagatttttaaaacaagttttaaaattctctcagtgttttgattattaatgaa...

Basic information

species Glycine max
transcript GLYMA06G42080.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42080.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv19s0177g00140.t01 (Vitis vinifera), 5'ss of exon 1
CAAGGCTGAGGATGCCATTGTGAGGCTCACTAGGGAGGTTGTGCCTGGCATGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattctattatctcttgatactcttgtgccacttattcaatttgagatttttaaaacaagttttaaaattctctcagtgt-tttgattattaatgaa
|| ||| |||||||  || ||||||||||| |||||||| ||||| || ||||| || || || ||||||||||| |||||||||||  | |||||||||||||  ||||  | ||||   |     || |   |||| ||   ||   ||     |      |    |||  ||  |   | | |||||  ||| |  | 
CACGGCAGAGGATGAGATCGTGAGGCTCACCAGGGAGGTGGTGCCGGGAATGATCGTCACCGGAATGGAAGTTGCAGAGATTGATGGCTCCCCAAGGATGgtaattttcttctttctcactacttgtttttagtactt-tttgtttcttgaaaaaaattgtttggacaaaagatcattagatatatttgaaaatttaaaat

upper sequence: GLYMA06G42080.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ04508 (Selaginella moellendorffii), 5'ss of exon 1
CAAGGCTGAGGATGCCATTGTGAGGCTCACTAGGGAGGTTGTGCCTGGCATGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattctattatctcttgatactcttgtgccacttattcaatttgagatttttaaaacaagttttaaaattctctcagtgttttgattattaatgaa
||  || ||||| || || |||||||||||| | |||||||| ||||| ||||| || ||||| |||||||| || ||||| ||||| || || |||||||||||    | ||   ||||  |  | |||| |  ||||  |  ||   | ||                                               
CACTGCCGAGGACGCGATCGTGAGGCTCACTCGCGAGGTTGTTCCTGGGATGATCGTCACTGGCATGGAAGTCGCGGAGATCGATGGGGCACCGAGGATGgtaaagaggtttttgttctttct-ttgttgtccgtcttaa-cgtttctcggttccag-------------------------------------------

upper sequence: GLYMA06G42080.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ26284 (Selaginella moellendorffii), 5'ss of exon 1
CAAGGCTGAGGATGCCATTGTGAGGCTCACTAGGGAGGTTGTGCCTGGCATGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattctattatctcttgatactcttgtgccacttattcaatttgagatttttaaaacaagttttaaaattctctcagtgttttgattattaatgaa
||  || ||||| || || |||||||||||| | |||||||| ||||| ||||| || ||||| |||||||| || ||||| ||||| || || |||||||||||    | ||   ||||  |  | |||| |  ||||  |  ||   | ||                                               
CACTGCCGAGGACGCGATCGTGAGGCTCACTCGCGAGGTTGTTCCTGGGATGATCGTCACTGGCATGGAAGTCGCGGAGATCGATGGGGCACCGAGGATGgtaaagaggtttttgttctttct-ttgttgttcgtcttaa-cgtttctcggttccag-------------------------------------------

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|58021386|gb|CX708127.1|CX708127
EST:     TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATG                         GGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
genomic: TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattct ... ttgaatgcagGGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
EST: gi|208328127|gb|GE124665.1|GE124665
EST:     ATTGATGGTGCTCCAAGGATG                         GGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
genomic: ATTGATGGTGCTCCAAGGATGgtaaaattct ... ttgaatgcagGGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
EST: gi|298165255|gb|HO011304.1|HO011304
EST:     TGATTGTTACTGGGATGGAAGTTGCTGGGATTGATGGTGCTCCAAGGATG                         GGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
genomic: TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattct ... ttgaatgcagGGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
EST: gi|17963372|gb|BM270122.1|BM270122
EST:     TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATG                         GGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
genomic: TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattct ... ttgaatgcagGGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
EST: gi|192311166|gb|FK004799.1|FK004799
EST:     TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATG                         GGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
genomic: TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattct ... ttgaatgcagGGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
EST: gi|192311165|gb|FK004798.1|FK004798
EST:     TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATG                         GGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
genomic: TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattct ... ttgaatgcagGGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
EST: gi|192309129|gb|FG999076.1|FG999076
EST:     TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATG                         GGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
genomic: TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattct ... ttgaatgcagGGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
EST: gi|192309130|gb|FG999077.1|FG999077
EST:     TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATG                         GGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
genomic: TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattct ... ttgaatgcagGGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
EST: gi|58024427|gb|CX711168.1|CX711168
EST:     TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATG                         GGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
genomic: TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattct ... ttgaatgcagGGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
EST: gi|298179311|gb|HO027782.1|HO027782
EST:     TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATG                         GGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
genomic: TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattct ... ttgaatgcagGGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG
EST: gi|192320272|gb|FK014258.1|FK014258
EST:     TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATG                         GGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATTTG
genomic: TGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattct ... ttgaatgcagGGTCCAACATTTGGAGCAATGATGATTTCAGGGCAAAAAGCAGCCCATCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGCTGAGGATGCCATTGTGAGGCTCACTAGGGAGGTTGTGCCTGGCATGATTGTTACTGGGATGGAAGTTGCTGAGATTGATGGTGCTCCAAGGATGgtaaaattctattatctcttgatactcttgtgccacttattcaatttgagatttttaaaacaagttttaaaattctctcagtgttttgattattaatgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG