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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgcttttctttcatgaattgttgatacttaatacttgggctttccgataaaagataacgttttttaaatctgacaaaatctgctgcagatagtggga...

Basic information

species Glycine max
transcript GLYMA17G00910.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00910.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 5
TGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgcttttctttcatgaattgttgatacttaatacttgggctttccgataaaagataacgttttttaaatctg---acaa-aatctgctgcagatagtggga
|| |||||||||   | || | ||| ||  |||||||| ||||||| || ||||| |||||||||||||| ||||| || || |||||||| || || |||| |||      ||| |   ||| |  ||| |  |  |   ||   |    |||  | |||     || |||  |   |||| | | |||     | ||||   
TGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGAAGCTAGgtctgcaaagtgttctt---ttggttgtacatcctgatacagcgcacaataaaagtacaacagaaatttaattggcaaacaatagtatgcgaggaaaagtgta-

upper sequence: GLYMA17G00910.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 5
TGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgcttttctttcatgaattgttgatacttaatacttgggctttccgataaaagataacgttttttaa--atctgacaaaatctgctgcagatagtggga--
|| |||||||||   | || ||||| ||| |||||||| |||||||||||||||| |||||||||||||| ||||| || ||||||||||| || || |||| |||  || || | ||   ||   ||| | |||| | | |||     | |  | || |   | || |   || ||  | |  |         || |      
TGTTTGCAGCACAGTCAATTCAATTGGGTATCAATGATATTGTTGTGGCTGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGAAGCTAGgtatgcaattattacttgg--tggatatattcaata-tcgagctgcataa-accaaatgatagtcttaagttatttggtagatacatgcatgcttacttatctt

upper sequence: GLYMA17G00910.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM5G830250_T01 (Zea mays), 5'ss of exon 3
TGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgc---ttttctttcatgaattgttgatacttaatacttgggctttccgataa-aagataacgttttttaaatctgacaaaatctgctgcagatagtggga
|| |||||||||   | || ||| | ||| |||||||| |||||||||| ||||| |||||||||||||| ||||| || ||||||||||| || || ||||   |   | || |||  || ||   |   |  | |  ||        |  || | ||  | | ||| ||||     || | |  |   |  |  || | |  
TGTTTGCAGCACAGTCAATTCAACTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGAAGCTAGgtacacaagtattattttgtggatacatctaatatcaggctgaaataaccgaattataatcttaagttatttag--tggatacatgcctgtttacttatttg--

upper sequence: GLYMA17G00910.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 5
TGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgct--tttctttcatgaattgttgatacttaatacttgggctttccgataaaagataacgttttttaaatctgacaaaatctgctgcagatagtggga--
|| | || ||||   | || ||  | ||| |||||||| |||||||||| ||||| |||||||||||||| ||||| || ||||||||||| || || |||| |||    | || || |||    |  |    |  | |  | || || | | |  | ||   |  || |    |  | |  | ||| |  |  || |   |  
TGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGAAGCTAGgtatgcaaagtactgtcttgatacatccag---tggtgccggtgcattaccaaagcatatcttgagttatttcacatataggagctgtt-tacttatttaaatt

upper sequence: GLYMA17G00910.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv18s0089g00570.t01 (Vitis vinifera), 5'ss of exon 2
TGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgcttttctt-tcatg-aattgttgatacttaatacttgggctttccgataaaagataacgttttttaaatctgacaaaatctgctgcagatagtggga--------------------------------------------------------------------
   |   ||   | |   ||       ||   |||||||| |||||||||||||| |||||||| ||||| ||||| ||||| ||| | |  || || | ||| ||||||    |||||  ||   | ||   || |   | |  |      |  || || |   |   ||  |   || ||   || ||  |  |||                                                                        
-TTTAAGAGGGTTGAGAGTAT------GTAAAAATGATGTAGTTGTGGCTGGTGGCATGGAAAGAATGTCTAATGCGCCTAAATACCTAGTAGATGCAACgttagctttttgggtcatgtgatcaattatgtctattgagttgcttgcttagtttaacatgattctcagtatgtg-aacgaagcatgttg-ggccagtacatattgttgccgttcttactaatagggagaagtgtctatgtatctaagctgactctgagcttataaacag

upper sequence: GLYMA17G00910.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv18s0089g00590.t01 (Vitis vinifera), 5'ss of exon 4
-TGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgcttttctt-tcatg-aattgttgatacttaatacttgggctttccgataaaagataacgttttttaaatctgacaaaatctgctgcagatagtggga
 || | |    |       |   | |  ||   |||||||| |||||||||||||| |||||||| ||||| ||||| ||||| ||| | |  || || | ||| ||||||    |||||  ||   |  |   || |   | |  |      |  || || |   |   ||  |   |||||   || ||  |  |||    
GTGATAGTT-TAAGAGGGTTGAGAGTATGTAAAAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTAGATGCAACgttagctttttgggtcatgtgatcaattttgtctattgagttgcttgcttagtttaacatgattctcagtatgtg-aacaaagcatgttg-ggccagtacat

upper sequence: GLYMA17G00910.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 4
TGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgcttttctttcatgaattgttgatacttaatacttgggctttccgataaaagataacgttttttaaatctgacaaaatctgctgcagatagtggga-
|| |||| ||||   | || ||||| ||| |||||||||| |||||||||||||| |||||||| ||||| ||||| ||||| ||| | |   | || ||||| |  |     | | ||||  | || |            |   |   | |||| ||||       |||   | | ||    |  |      | ||    
TGTTTGCTGCACAGTCTATCCAATTGGGTGTCAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatggaaatta-gaatcttggaaatcattcgaagatgacatttaaaaaaaaataaaaaaaaataataataaaaacgaatcttagcatcaatgaagc

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|213587273|gb|DB965935.1|DB965935
EST:     GGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAG                         GAAAGGGTCTCGGTATGGACATGATACCATCATTGA
genomic: GGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgctttt ... tctaaaacagGAAAGGGTCTCGGTATGGACATGATACCATCATTGA
EST: gi|9986219|gb|BE660327.1|BE660327
EST:     GGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAG                         GAAAGGGTCTCGGTNTGGACATGATACCATCATTGATGGTATGGTCAAAGA
genomic: GGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgctttt ... tctaaaacagGAAAGGGTCTCGGTATGGACATGATACCATCATTGATGGTATGGTCAAAGA
EST: gi|298194892|gb|HO043364.1|HO043364
EST:     GGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAG                         GGAAGGGTCTCGGTATGGACATGATACCATCATTGATGGTATGGTCAAAGA
genomic: GGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgctttt ... tctaaaacagGAAAGGGTCTCGGTATGGACATGATACCATCATTGATGGTATGGTCAAAGA
EST: gi|192294916|gb|FG986639.1|FG986639
EST:     GGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAG                         GAAAGGGTCTCGGTATGGACATGATACCATCATTGATGGTATGGTCAAAGA
genomic: GGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgctttt ... tctaaaacagGAAAGGGTCTCGGTATGGACATGATACCATCATTGATGGTATGGTCAAAGA
EST: gi|19452347|gb|BM953757.1|BM953757
EST:     GGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAG                         GAAAGGGTCTCGGTATGGACATGATACCATCATTGATGGTATGGTCAAAGA
genomic: GGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgctttt ... tctaaaacagGAAAGGGTCTCGGTATGGACATGATACCATCATTGATGGTATGGTCAAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgcttttctttcatgaattgttgatacttaatacttgggctttccgataaaagataacgttttttaaatctgacaaaatctgctgcagatagtggga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagata