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

...atagggttttatttcttattaattataattcatctagttgtttctaatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

Basic information

species Glycine max
transcript GLYMA17G07290.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 2
atagggttttatttcttattaattataattcatctagttgtttctaatttatatttattgttagtttcata---taattgattgatgcac-atacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
 ||   |||| ||   |||    |  || |     |  | | | |    ||| ||  ||| | | || | |   |  |   || |   |  | || | | ||||||| |||||||||||||| |||||||| ||||||||||||||||| |||||  | || || |||||||||||||||
-taaattttttttgtgtatatccttgaaattgcaaaaatatgtttg---tatcttagttgctcgatttagaggttgctcacttaacaaatgacacatattgcagTGTCATTGTGGAAGCTCTTAAGGTGGATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT

upper sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
atagggttttatttcttattaat-tataattcatctagtt-gtttctaatttatatttattgttagtttcatataattgatt--gatgcacatacttttc-gcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
       ||   |  | |||| | || |  ||| |  ||  |    | | ||   | | |||||  | |   || |||  ||  | | | | |  || || ||||||| ||||| |||||  | |||||||| ||| |||||| ||||||||||||  | ||||| |||||||||||||| 
-----ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG

upper sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 2
----atagggttttatttcttattaa-ttataattcatctagttgtttctaatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
     | |  |    |||  | |||| |||| | | |   | |  |   | |  |||    |   |   |||  | |||  | |   |     |||  |  ||||||| ||||| |||||  | |||||||| ||| |||||| ||| |||||||| || ||||| |||||||||||||| 
cttgcttgcttggcgttttattttaacttattaataacagaataatcggtgacctat---cacattctatttgttgtaaacggtctgtctgtctaccat--gcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA

upper sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 2
-----atagggttttatttcttattaattataattcatctagttgtttctaatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
      |  |  |||| |  | | | |   |  || ||| |      |  |||| | | | |    ||  ||  | |  ||  || | | |   || |||  |||||| |||||||||||||| ||| |||||||||||||||| || || |||||  | || |||||||| || ||||||
attttcttagagtttagtgataagttacagtttttaatccaccacccttcaattcaaact-acaaatatatttgt-tgcttagttaacgaa---acatttttcagTGTCATTGTGGAAGCTCTCAAGATGGACAGTTTGCAGAAACTCTGTTCATCGCTCGAGCCCATTCTCCGAAGAGTT

upper sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 2
-----------atagggttttatttcttattaattataattcatctagttgtttctaatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
            ||| |||| |||  |   |  |  |  || |||||    | |  ||  || |  ||| ||| ||| |      ||   | | | |   || |||  |||||| |||||||||||||| ||| |||||||||||||||| || || |||||  | || || ||||| || ||||||
aagtaaatttggtagagttt-attggtaggttctggtttttgatctaccgctcttcaaactacaaatat-gtttgttgc------ttagctaacgaa---acatttttcagTGTCATTGTGGAAGCTCTCAAGATGGACAGTTTGCAGAAACTCTGTTCATCGCTTGAGCCTATTCTCCGAAGAGTT

upper sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
atagggttttatttcttattaa---ttataattcatc-tagttgtttctaatttat-atttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
    || | | || ||| ||     || || || | | || |  |  | || | || |  |||       |   | ||| | ||   |  |  |||  |  ||||||| ||||| |||||| | ||| |||| ||| |||||| ||| ||||||||  | ||||| |||||||||||||| 
---tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccct--gcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA

upper sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------atagggtttt---atttcttattaattataattcatctagttgt--------ttctaatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
                                         || | ||| |   || | | ||| |||   | |  | |   ||         || | || |||||| |||||  ||   || | |   | |  || |  |  || | |||||||||||||||||||  ||||| |||| ||||| |||| |||||| || ||||| ||||| ||||||||  |||| 
gtaatttgtgttgatgcttgtaatttttctgattattgattatggcgttgttgaatctgtaattgatttgtagttgtatgaatgaaaaaagggttgttatgtatattgattgtctgtgg-atttgagaaagttgtgtatgtg-ttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG

upper sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 2
atagggttttatttcttattaattataattcatctagttgtttctaatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
 ||      || ||||| ||| | | |||  ||  |  ||||||     || |   ||   |   ||    | ||   ||| |   ||         |||||| ||||| || |||||||| || || |||||||||||||||||||| ||||| ||||| ||||| ||  |||||
gtaattcactagttcttcttactgaaaatatatacaactgtttc-----tacaaaaatctctgactttg-gttatcttttggtttgcac--------cagTGTGATTGTTGAGGCTCTGAAAGTAGATAGTTTGCAGAAGCTTTGCTCCTCTTTGGAACCTATTCTCCGCCGAGTT

upper sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 2
atagggttttatttcttattaattataattcatctagttgtttctaatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
         |   | |   | ||| |||  ||  | ||| ||   | ||| |   ||||      ||  | |  |    |  |||   |  | | |||||||| ||||| || |||||||| || ||||||||||||||||||||||| ||||| ||||| || || ||  |||||
--------gtgagtttctctgattttaac-cagattgtttttgaaagtttcttagtattaaagactttttctggtc--ctattgctttttgtctgcgcagTGTGATTGTTGAGGCTCTGAAAGTTGACAGTTTGCAGAAGCTTTGCTCGTCTTTGGAACCTATCCTCCGCCGAGTT

upper sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
atagggttttatttcttattaattataattcatctagttgtttctaatttatatttattgtta-gtttcatataattgattgatgcacatacttttc--gcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
 |  |   ||   | || |  |||| ||    | |    || || | || | | ||||| ||| ||    | ||||  | | | | | |||  | ||  |||||||||| ||||||||||| |||||||| ||| ||||||| ||||||||||| || ||||| |||||||||||||||
-tttgcccttgcctgtt-tctatta-aacctctatgaacgtctcaatttaacacttatttttatgtcagttctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT

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|213592784|gb|DB957828.1|DB957828
EST:     GAGGGTGGAGAAGATGACCAGCCTGAACGAAAGAGGCCTGCTCTTGCCAG                         TGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATC
genomic: GAGGGTGGAGAAGATGACCAGCCTGAACGAAAGAGGCCTGCTCTTGCCAGgtaaattaat ... cttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATC
EST: gi|209719983|gb|BW651078.1|BW651078
EST:     GAGGGTGGAGAAGATGACCAGCCTGAACGAAAGAGGCCTGCTCTTGCCAG                         TGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATC
genomic: GAGGGTGGAGAAGATGACCAGCCTGAACGAAAGAGGCCTGCTCTTGCCAGgtaaattaat ... cttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
                                           tacttttc  CT-rich tract
     atatttattgttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagggttttatttcttattaattataattcatctagttgtttctaatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC