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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaagcatagtttgacaataatgcattctagttcactcttctagtttgtatgcaactcaactaacatctgggagtgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG

Basic information

species Glycine max
transcript GLYMA19G30450.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g03734.1 (Oryza sativa), 3'ss of exon 5
gtaagcatagtttgacaataatgcattctagttcactcttctagtttgtatgcaactcaactaacatctgggagtgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
                      | ||| |  ||   | ||| |  | |||  ||| |    |  |         |  |   |  |||||||||     ||| ||||| |||||||||||  | ||||||| |||||| ||  | |||||   | | ||||| |||||||| |||||||||||||||| ||| ||||||||
----------------------gtattatgattg--ttttccaactggtaatcaattttggttgccctgtaatttaatcgctggcattacatt-tggcagGGGGTTGCTTTGTTGAAGGCAATTGGTTAAAAAATGCGTTCAGGTGGAAGGAAACTATTGGTCCATGGGAAGAGAGACCTGGGCACTATGGAGATGTTTG

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g20420.3 (Oryza sativa), 3'ss of exon 7
gtaagcatagtttgacaataatgcattctagttcactcttctagtttgtatgcaactcaa--ctaaca-tctgggagtgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
   |  ||   ||| ||||  | |||  | ||| | | || | |||||       ||      | | | |       ||    | ||  ||   || |   ||| ||    | |||    ||| | |  |||   || ||||| || ||||    | |||||||||| ||||| ||||||||||| ||||||  |||||||||
aagaaaatgcattg-caatc-tccatcatggttaaatattgt-gtttgctaattgcttggtgttgataatgcacttatgcatatgtttcttttttttctgcagGTGGAAACTATGTCATGGGAAATTATTTACTGAACGCATTCCGGTGGAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTG

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 19
gtaagcatagt-ttgacaataatgcattctagttcactcttctagtttgtatgcaac---tcaactaacatctggga---gtgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
||| |||  || ||  ||    |  | || |||||    |  | |    |||   ||   |  |   |  | |  ||    || ||  || |||   | | |  |||| ||||||||||| ||||| || ||| |||||||||||||  |||||| |  ||| ||||| |||||||| ||||| ||||| ||||| || ||||||||
gtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattacgtgttcatagatgtttcagatatttgatagattccatgcgactactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAATCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G006130_T02 (Zea mays), 3'ss of exon 7
gtaagcatagtttgacaataatgcattctagttcactcttctagtttgtatgcaac---tcaactaacatctgggag---tgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
       |  ||| ||| |  |  | || |||||    |  | |    |||   ||   |  |   |  | |  ||    || ||  || |||   | | |  |||| ||||||||||| ||||| || ||| |||||||||||||  |||||| |  ||| ||||| |||||||| ||||| ||||| ||||| || ||||||||
----ctgtgttttcacatt--taaaatcaagttcttcatgtttggacatatattacgtgttcatagatgtttcagatatttgatagattccatgcgactactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAATCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 7
gtaagcatagt-ttgacaataatgcattctagttcactcttctagtttgtatgcaac---tcaactaacatctggga---gtgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
||| |||  || ||  ||    |  | || |||||    |  | |    |||   |    |  |   |  | |  ||    || ||  || |||   | | |  |||| ||||||||||| ||||| || ||| |||||||||||||  |||||| |   || ||||| |||||||| ||||| ||||| ||||| || ||||||||
gtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattatgtgttcatagatgtttcagatatttgatagattccatgcgactactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAGTCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 6
gtaagcatagtttgacaataat-gcattctagttcactcttctagtttgtatgcaactca---------actaa--catctgggagtg-----ttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
||| ||   || |     || |   | ||  |||| |  | |||   |||||   |   |         | |||  ||| |  |  |       ||  || ||| |   |    |||| || || ||||| ||||| |  |||||||||||||| ||| | |||| |  ||| ||||| |||||||| ||||||||||| ||||| || ||||||||
gtatgctccgtgttttcttatttagaatcaggttcccaatgctaagatgtatatgatatattgcaatatattaatacatttaaggataatggactagattgcatgatgctattgtagGAGGCTGCTTTGTAGAAGGTGGCTGGTTAAGAAATGCCTTTAGGTGGAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTG

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G097277_T01 (Zea mays), 3'ss of exon 6
-gtaagcatagtttgacaataatgcattctagttc-actc---ttctagtttgtatgcaactcaactaacatctgggagtgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
  | | |||| ||    | |  | |||  ||  |  | ||   ||  |   |||||  |   ||| |   || ||  ||  |   |    |  |  ||   ||||| ||    | ||     ||| | |   || ||||||||||||| ||||      |  | ||||||||||||||||||||||| ||||||  |||||  ||
gtttatcatatttgattattcttacatcatatctggagtcaagttaaacactgtatctattgcaa-tggtatgtgtaagattctgtacctaccatgtt---ttagGTGGCAACTATGCCATGGGAAATTATCTACGAAATGCATTTCGGTGGAGTGAGACTGTGGGACCATGGGAGGAGAGACCTGGTCACTTTAATGATGCCTG

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------gtaagcatagtttgacaataa---tgcattctagttcactcttctagtttgtatgcaactcaactaacatctgggagtgt-tatttttcatt----acatt----gcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
                               || | | || | |  | |||    | | |  ||||||| | |   |    | ||| |  | |  | | ||  |  |  || |||| || | |    | |||       ||||| ||||||||||| || || ||||||||||| ||||| || || ||||||  | || | ||||| ||||| |||||||| || || ||||||||||||||
gtacgtattatttaaggctagtagcatttttgtta-cttattctatccatagacgtacctcttagttcaatatgacaaaaagcatg-acttaagatgaaataagctaaagtctattctttactctggatatttgtgaatttagGTGGTTGTTTTGTCGAGGGTGAATGGTTAAGTAATGCCTTCCGCTGGAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTG

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
gtaagcatagtttgacaataatgcattctagttcact--cttct-----agttt---gtatgcaactcaactaacatctgggagtgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
          |      |||||   |||| ||||  |  |||||     ||  |   | ||       || |||  || |  | | |  | | |  ||| ||||||| ||| || ||||| |||||||| || |||||||||||||||||||| ||||||    | ||||| || ||||||||||||||||| |||||||||||||||||
--------catccattcataatattttctggttccatgacttcttccgaaggctcaggcatttggtcgaattaat-tcagataatatgttctctatttatattgcat-agGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG

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|9820378|gb|BE555888.1|BE555888
EST:     CCTTGTTGAAATGCTGACAGCTTTGAAACCAAGATTTATCAGATTTCCGG                         GCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAA
genomic: CCTTGTTGAAATGCTGACAGCTTTGAAACCAAGATTTATCAGATTTCCGGgtatgcataa ... attgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAA
EST: gi|24136140|gb|BU926650.1|BU926650
EST:     CCTTGTTGAAATGCTGACAGCTTTGAAACCAAGATTTATCAGATTTCCGG                         GCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAG
genomic: CCTTGTTGAAATGCTGACAGCTTTGAAACCAAGATTTATCAGATTTCCGGgtatgcataa ... attgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtatgcaactcaactaacatctgggagtgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
             aactaac  putative branch site (score: 1)
                               ttatttttcattacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatagtttgacaataatgcattctagttcactcttctagtttgtatgcaactcaactaacatctgggagtgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - gcattct
- - - - - - - - - - - - - - - - - - -cttctag
- - - - - - - - - - - - - - - - - - - - - - - -gtatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggagtg