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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttaagctatttgtttgtttttcccttttatggccttggtgccatccttttgcattatctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG

Basic information

species Glycine max
transcript GLYMA20G30250.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g45670.1 (Oryza sativa), 3'ss of exon 1
atttaagctatttg-tttgtttttcccttttatggccttggtgccatccttttgcattatc---tcatat-tgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
      ||| ||   ||    | ||  |   |  |  ||| |       | | | | | ||   | | || || | ||  | | |  | | |   |   | |||| ||||| ||||| ||||||||||| ||||| ||||||||||| ||||| || || |||
-----tgctgttgaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacatctgatattcatgtgtaataccttgcttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG

upper sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g01670.1 (Oryza sativa), 3'ss of exon 1
---atttaagctatttgtttgtttttcccttttatggccttggtgccatccttttgcattatctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
     ||  |  |    ||     |    |||||   |    |    ||  ||      ||  |   ||| |||   || |||  |   |  | || || ||| ||||| ||||| ||||||||||||||||||| |||||| || ||||| || || |||
ttatcttgtggcaaacattacgagtggggttttaccacaactgaaaaatggttccttcctactt---attctttgcattctttacttgcttttactataacagGTTTGATCGTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG

upper sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 1
---------atttaagctatttgtttgtttttcccttttatggccttggtgccatccttttgcattatctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
         |||| |  || ||||    |    | | | |      ||| ||     | || |||  | |  |||   |  || ||| | ||| |       ||| ||| ||||||||||||||||||||||||||||||| |||||| || |||||||| || |||
tttaagggcatttca--tacttgtagaatgcctcatgtcacacatctggagcagctttcttacatattatgctataaatccttctttcttttcgt-------gtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG

upper sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G118693_T02 (Zea mays), 3'ss of exon 1
atttaagctatttgtttgtttttcccttttatggccttggtgccatccttttgcattat-ctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
 ||   |  ||   |    | | ||     || | |   |    ||       |||  | |   || | ||  | | |    |   ||| ||   | |||| ||||||||||||||||| ||||| || || |||||||| || ||||| |||||||||
gttcttga-atccatacactgtcccaaaaaattgtcactgaaatataagaccacatcttgcatgtaatattcatgtgtaaactattttcttttcttttcagCTTTGACCGTGACTGGAAGAAGATAGAGGCTTTTGTTGGCTCCAAGACCGTCATCCAG

upper sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G833032_T03 (Zea mays), 3'ss of exon 1
----atttaagctatttgtttgtttttccctttta-tggccttggtgccatccttttgcattatctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
     || || | ||     |||        |||| ||   |    | |    | ||||||  |   || |  | | |    | |||| |||   | |   | || ||||| ||||||||||| ||||| || || |||||||| || ||||| |||||||||
tgttcttgaatccatacacatgtcccaaaaatttagtgaaatataagaccatatcttgcat-gtaatat-tcatgtgtaaactatgtttcttttcttt---ttagCTTTGATCGTGACTGGAAGAAGATAGAGGCTTTTGTTGGCTCCAAGACTGTCATCCAG

upper sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G52660.2 (Arabidopsis thaliana), 3'ss of exon 1
---atttaagctat-ttgtttgtttttcccttttatggccttggtgccatccttttgcattatctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
   ||     | || ||         |       ||| |  |       |  ||| |   |   || |  | | | || | |||||   || |||   | | || |||||  | |||||||| ||||||||||| ||| |||| ||||||||||| || |||
gtgatgcgtacaatcttaggcaaggattagacacatg-ctatatccaggttgtttggtggtggatc-tgatatctcttatgtttgtgttttgatt--attttagGTTTGATAGAGACTGGAAGAAGATTGAAGCTTTTATTGGTTCAAAGACAGTGATTCAG

upper sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
----atttaagctatttgtttgtttttcccttttatggcct-tggtgccatccttttgcattatctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
    ||       ||  || | | ||| |  |||||  | | |  | ||    |  || ||||  |   ||   ||  |||| || ||     |||||   |||| ||||||||||| |||||||||||||| ||||||||||||||||||||||| || |||
aatcatcaccagaatgggtgtatcttttcagtttatctcttcttattcctaattaatggattagtttccataaattgattttgttattg----attctac-tcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG

upper sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
atttaagctatttgtttgtttttcccttttatggccttggtgccatccttttgcattatctcatattgttttttttttttgttcctt---cattctgtat---cagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
  |  ||         ||  |||    |  |  || |  ||| || ||||| |    |  | | | ||   | |  |   | |       || ||||  |   ||||||||| || |||||||||||||||||||| || ||||| || ||||||||||| |||
--tggagtaggaaaactggattt----tagaatgcttaagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgcttttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG

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|22524646|gb|BU083457.1|BU083457
EST:     GAGAGTTGGACCGAACCTGAGCACGACAAGTTCCTCGAAGCTCTTCAGTT                         ATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGT
genomic: GAGAGTTGGACCGAACCTGAGCACGACAAGTTCCTCGAAGCTCTTCAGTTgtatgtgaat ... tctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGT
EST: gi|22524561|gb|BU083372.1|BU083372
EST:     GAGAGTTGGACCGAACCTGAGCACGACAAGTTCCTCGAAGCTCTTCAGTT                         ATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGT
genomic: GAGAGTTGGACCGAACCTGAGCACGACAAGTTCCTCGAAGCTCTTCAGTTgtatgtgaat ... tctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttgcattatctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
             tctcatattgtttttt  CT-rich tract
         attatctcatattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttaagctatttgtttgtttttcccttttatggccttggtgccatccttttgcattatctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - tgtttgt
- - - - - - - - - - -ttccctt
- - - - - - - - - - - - - - - - ggccttg
- - - - - - - - - - - - - - - - - - - - tgccatc
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcatta