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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttatacattatactatatataatttgtgttgatgaacaaaatacaaccctacattataatatgcactgtttactttttctgaacactggttttgtttcttcctttctccaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTCTTGAGGTGGTCCGA

Basic information

species Glycine max
transcript GLYMA10G34240.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os09g39690.1 (Oryza sativa), 3'ss of exon 6
----gtatttatacattatactatatataatttgtgtt-gatgaacaaaatacaaccctacattataatatgcactgtttactttttctgaacactggttttgtttcttccttt----ctccaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTCTTGAGGTGGTCCGA
    | | | || | ||       | |||||   |  | | |  |   | |     | |   | |||   |  |      | |  |  |||    | ||||||  ||||  ||      |      |  | |||||  ||||||||||||||||||||| ||||||||||| || ||||||||  ||||  | || || ||||| ||  | ||||| ||||| ||  |||||||| |||||
gtttgaactcatgcttttcttctgaaataatgaataataggtccatgtagtttgttcttctctaatacagtataac----agtactaatgatggtttgttttgcctctttgttgggggttggggtgttgactttctatcagATGTGGGCACATGTGCACATGTTCAAAATGCGCGAATGAGTTGGTTCGAAGCGGAGGGAAATGCCCGCTGTGCCGTGCACCCATAATTGAGGTGATCCGA

upper sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g57750.2 (Oryza sativa), 3'ss of exon 5
gtatttatacattatactatatataatttgtgttgatgaacaaaatacaaccctacattataatatgcactgtttactttttctgaacactggttttgtttcttcctttctccaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTCTTGAGGTGGTCCGA
                           |    || |  | | ||| |    |  | | | | || |  |||  |  ||     |      | || |  | |  |  |    || | |||    |  |  |||||| ||||||||||| ||||| ||||||||||| || ||| |||||||  ||||||| ||||| ||  |||||||||| || ||    |||||||| || 
--------------------------gtcagcttcac-agctaaacatg-tctgatactttgatgt-tactaatctctaaccttt----tttgtctgatgtacttgtaaaacccatttggtgatggtgacagATGCGGGCACATGTGTACTTGCTCAAAATGTGCAAACGAGCTAATTCGCAGTGGTGGCAAATGCCCACTATGCCGAGCGCCGATCGCGGAGGTGGTTCGG

upper sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G006965_T01 (Zea mays), 3'ss of exon 6
gtatttatacattatactatatataatttgtgttg-atgaacaaaatacaaccctacattataatatgcactgtttactttttctgaacactggttttgtttctt--cctttctccaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTCTTGAGGTGGTCCGA
                          ||||  | | ||  || | || | |   |  |||   |   |   ||  | | |  |||  |   ||||  |   | |   ||| | |      |  | |      |||||||||||||||||||||||| || ||||| || || || ||  |||| ||||| || ||||| || || ||||| ||||| ||  | |||||  |||||
-------------------------gtttggctcgcattgaccacattctattatttattg-gacgagtgttgaat-catagtctatatgttggtagtagctgtgaacctgttttttgtgtttattactgatcagATGTGGGCACATGTGCACTTGCTCGAAATGCGCAAACGAATTGGTTCGAGGTGGAGGGAAATGCCCGTTGTGCCGCGCACCCATAATCGAGGTCATCCGA

upper sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 6
------------------gtatttatacattatactatatataatttgtgttgatgaacaaaatacaaccctacattataatatgcact--gtttactttttctgaacactggttttgtttcttcctttctccaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTCTTGAGGTGGTCCGA
                  ||  || | |  | |   || |||  ||| | || || |  |          |||  ||   |    |  |   |||  | || |||     |    || | | | |  |  |||       ||     |||||||||||||||||||||||||||||||||||||| ||||||||  |||||||||| || || || || || |||||||| || ||| |||||||  |||||
gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttatcagaacctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttccccttatctttactgtcttccgttgaaaaaaaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA

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|193417322|gb|FK383798.1|FK383798
EST:     GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTATAG                         ATGTGGGCACATGTGCACTTGTT
genomic: GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTATAGgtatttatac ... tttcttgcagATGTGGGCACATGTGCACTTGTT
EST: gi|193623976|gb|FK573856.1|FK573856
EST:     GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTATAG                         ATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAA
genomic: GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTATAGgtatttatac ... tttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAA
EST: gi|298171118|gb|HO016150.1|HO016150
EST:     GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTATAG                         ATGTGGGCACATGTGCACTTGTTCAAAATGCGCCAATGAGTTAATTCGTGG
genomic: GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTATAGgtatttatac ... tttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGG
EST: gi|208254365|gb|GE052115.1|GE052115
EST:     GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTATAG                         ATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGG
genomic: GGAACTTGCTGTGTTTGTTGTGATAACCATATCGATTCTCTTTTGTATAGgtatttatac ... tttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctgaacactggttttgtttcttcctttctccaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTCTTGAGGTGGTCCGA
                                             tttcttgc  CT-rich tract
                ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttatacattatactatatataatttgtgttgatgaacaaaatacaaccctacattataatatgcactgtttactttttctgaacactggttttgtttcttcctttctccaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTCTTGAGGTGGTCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG