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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCTTCACCGCATCAATGGAGTTGGACGGCGTTCTCCTCGGCATGTGCAACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgcctcacatttttttctctctttcttttgttactattattaattattcttaataatgtcatgagtattgagtagtatattactattttgagc...

Basic information

species Glycine max
transcript GLYMA13G20780.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 1
CCTTCTTCACCGCATCAATGGAGTTGGACGGCGTTCTCCTCGGCATGTGCAACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc-ctcacatttttttctctctttcttttgttactattattaattattcttaataatgt-catgagtattgagtagtatattactattttgagc
           |    ||||| ||  || ||||| ||||| || ||| ||||||| |||||||||||||| ||||||||||||||||| ||| |    |||||     || |||   |  |  |    |||  |  || | |||    | ||   | ||  |  | | | |     ||  |  ||   ||   ||    |  
AGCGGAGAGTAGAGGGAATGGCGTCCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGACGCCTTCCTCACCAAgtacgcgcgcgctcgtctcctcctgctccttagtcctgat-ctaccgctgatcccttttttttttttgccttttcgttttgc-gttcgtttggatccgaatg

upper sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 5'ss of exon 1
CCTTCTTCACCGCATCAATGGAGTTG-GACGGCGTTCTCCTCGGCATGTGCAACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgcctcacatttttttctctctttcttttgttactattattaattattcttaataatgtcatgagtattgagtagtatattactattttgagc-
           | |     | || |  || ||||| ||||| |||||| | ||||| |||||||||||||| |||||||||||||| || ||| |   ||||||| |    | |  |      |||   | |  | |  |  | |  |  ||||      ||  | ||   ||| |  |  | | || |  | |    |   
-AGGGAAGGATGGAGAGCGGAAGCTACGAGGGCGTCCTCCTGGGCATGGGAAACCCCCTCCTCGACATCTCCGCCGTCGTCGACGAGGCCTTCCTCGCAAAgtatgaaccaccccaacagccctcttcgtgtgctgtaatgatctc-tcgattaaaacctatggtctctgtagtctgtaagactgtactcttctgccaattt

upper sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G540538_T02 (Zea mays), 5'ss of exon 1
CCTTCTTCACCGCATCAATGGAGTTGGACGGCGTTCTCCTCGGCATGTGCAACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgta-----ttactgcctcacatttttttctctctttcttttgttactattattaattattcttaataatgtcatgagtattgagtagtatattactattttgagc
           | |     || |   || ||||| ||||| || ||| ||||||| |||||||||||||| ||||||||||| ||||| ||| ||  ||||||     |     |||| |  | |  | |||  |   ||| |    |||   | ||| || || |  |    |     |||  |    |  |  |  | ||   
GGAGAAGAGAGGAAATGGCGGCGACCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTCGTCGATGACGCCTTCCTGACAAAgtaagcggtcgtaccctcgccctctcgtgtctgatctgtttataggaattg--agttactcctagtcgtagtgttttggttgctttcggtggttttgctatg---

upper sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 1
CCTTCTTCACCGCATCAATGGAGTTGGACGGCGTTCTCCTCGGCATGTGCAACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgcc-tcacatttttttctctctttcttttgttactattattaattattcttaataatgtcatgagtattgagtagtatattactattttgagc
           | |     || |   || ||||| ||||| || ||| ||||||| |||||||||||||| ||||| ||||| ||||| ||| ||  ||||||   | | | || |     | |||| || |  | ||||  ||  | | | |  |  |  || ||   ||  |  |        | || |    | |   
AGAGAAGAGAGGAAATGGCGGCGAGCGAGGGCGTGCTCCTGGGGATGGGCAACCCCCTCCTCGACATCTCCGCCGTTGTCGATGACGCCTTCCTGGCAAAgtaagtcggtcgtctctcacctctctcactctgatctgtttataggaattactcctagtcgtagtggtctggttgctttcggcggttttgcggcctagtc-

upper sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 5'ss of exon 1
CCTTCTTCACCGCATCAATGGAGTTGGACGGCGTTCTCCTCGGCATGTGCAACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgcctcacattttttt-ctctctttcttttgttactatt--attaattattcttaataatgtcatgagtattgagtagtatattactattttgagc
|||  |  | | | |||||||  |  || ||  | ||||| |||||| ||||||| ||||||||||| ||| | ||||||||||| |  ||| | |||| |||   || |    | || || | |  |   || |    | || ||  | |  |   | || ||  |||  |   | |||  |    | |||   || ||   
CCTCTTGGATCTCTTCAATGGCTTACGAAGGAATCCTCCTGGGCATGGGCAACCCCCTCCTCGACATTTCTTCTGTCGTCGACGAAGAATTCCTTCAAAGgtaactctactctcctttgttctgcggttcgtcgtcctctgcttttcaaatgctgcgttttgattctgtttttgttcttggatccgttcttatggttgtg---

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|209708530|gb|BW668141.1|BW668141
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|209710379|gb|BW681278.1|BW681278
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|13311384|gb|BG405035.1|BG405035
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|192324906|gb|FK016092.1|FK016092
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|208250133|gb|GE044958.1|GE044958
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|12773339|gb|BG238266.1|BG238266
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|213598835|gb|DB968306.1|DB968306
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|209711575|gb|BW676820.1|BW676820
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|13477616|gb|BG507425.1|BG507425
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|4437142|gb|AI523007.1|AI523007
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|209711086|gb|BW681150.1|BW681150
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|151405346|gb|EV275160.1|EV275160
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|192327273|gb|FK019550.1|FK019550
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|151404672|gb|EV274486.1|EV274486
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|11687342|gb|BF594982.1|BF594982
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|208207845|gb|GE008088.1|GE008088
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|213611486|gb|DB959196.1|DB959196
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|9987590|gb|BE661698.1|BE661698
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|213597865|gb|DB958246.1|DB958246
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|19937792|gb|BQ081423.1|BQ081423
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|298174188|gb|HO017524.1|HO017524
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|12773014|gb|BG237941.1|BG237941
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|14126129|gb|BG790567.1|BG790567
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|213591667|gb|DB969767.1|DB969767
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|213587888|gb|DB959712.1|DB959712
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACACTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|213605470|gb|DB964609.1|DB964609
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|4395913|gb|AI494910.1|AI494910
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCGCTGAGGATAAGCACAAACC
EST: gi|193492538|gb|FK455704.1|FK455704
EST:     AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAA                         ATACGGTATCAAGTTGAACGATGCGATTCTCG
genomic: AACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgc ... tgtgtgacagATACGGTATCAAGTTGAACGATGCGATTCTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTCTTCACCGCATCAATGGAGTTGGACGGCGTTCTCCTCGGCATGTGCAACCCTCTCCTCGACATCTCTGCCGTCGTCGACGACGCTTTCTTGCAAAAgtattactgcctcacatttttttctctctttcttttgttactattattaattattcttaataatgtcatgagtattgagtagtatattactattttgagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC