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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

Basic information

species Glycine max
transcript GLYMA13G43680.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 11
agaagtgagttttaaaacaatagtccttattgctggttcaat-tatcaacaatatttgtttcatgg---gtggtgacttattgttgatt-taatttgttg--tgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
        ||||| |||   || |  |    | |   | ||| |    |   | | |   |  |||    || |  | | || || ||  || | | ||   | |||| ||||| ||||||||||||||| || ||||||||||| ||||||||||| || ||||| || ||||| |||||||||||||||||||| ||||| || |
------cggttttgaaattgtacttgtcgg-gttaaataaatgtgatgaacttttctacgttctggtttatgtttgcatgttattaataatagtgtattcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACCGCATTGGCATGGAGAAATAGATCATTCGGGT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
agaagtgagttttaaaacaatagtcc-ttattgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatttgttg--tgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
 ||      | ||  |  || | |   ||| |      || | |||  |   || || |    |  ||    | |||| ||   | || | | ||   | ||||  |||| ||||||||| |||||||| ||||||||||| ||||||||||| || ||||| || ||||||||||| |||||||||||||| ||||| || |
-gattctgttgttgtagtaaaattaaattaatctcaaatctagtat--agtgtaattatagtgtatgttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtg-----acttattgt---tgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
        | |  || |      | |||  | || | | |||  |      |  |  | || ||  | ||       |||| | |   | || |  ||  |||  ||||  |||||||| || || ||||| || ||||| || || |||||||||||||| | ||| || || ||||||||||| ||||| |||||||||||||| |
-------ggctacaacatttcttttctttctactaggt-aatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 11
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtgac-ttattg-----ttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
    ||  |  |||  |  ||  |  |||   || |||   |  |||   |||| | |||  ||   | | || |||||       || | | || | |  | ||||  ||||  |||||||| |||||||| ||||||||||| ||||||||||| || ||||| |||||||| ||||| |||||||||||||| |||||||| |
----gtttgaattatcatgat--tttttaaaacttgttttgtggtcatgtatatcttttttgtgctggtttacattattaatatactggtgtgatatttgtttcagAGCTTAAGACACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATATACACAGCATTAGCATGGAGAAATAGATCATTTGGGT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
-----agaagtgagttttaaaacaatagtcctt--attgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
       | |  ||    ||  ||   ||  ||  |  | | |||| |   |   | |   |  ||| |      || ||| ||  ||  | |  | |    | |||| ||||  |||||||||||||||||||||||||| ||| ||||||||||| ||||||||||| ||||| ||  | |||||||||||||| || ||||| |
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggat-atttaaaaaacagtaactaatcctt--tctgttct----tccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtgacttat-tgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
     ||| ||||   | ||      || |  |  |   |       |   |||||||   |     ||| | | || |  || | | || | |  | |||| ||||| ||||||||| |||||||| ||||| ||||| ||||||||||| || ||||| |||||||| || || ||||||||||| || |||||||| |
-atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagtttaggttaatgatatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 10
-----------------------------------------------------------agaagtgagttttaaaacaatagtcctt--attgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatt-taatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
                                                               |||  ||||||    | |    ||   ||  |  ||   |  |   || | | |||  | |      ||| || |  || ||| |  || ||||  ||||  || ||||| ||||| |||||  |||| |||||||| |||||||||||||||||||| || || |||||  |||| ||||| |||||||||||||| |
gtacttttggatgctgatgtgttctttgtattttaaaacttgttactattgtaggtttatagtgtggtttttaagtggacatcttttcgttttattatttggtggtgctcattttgtgtggcgtataatctga-ttgtgattaattatttttggttggtcagAGCTTGAAGCATAATCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGTGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGGTCATTTGGAT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaa--caatatttgtttcatgggtg-gtgactt-attgt---tgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
         |    | ||   |  || |   |  |  ||    | |    |     || |||||    ||  | |  | |||||   | ||    || ||||  ||||  || ||||| || || |||||  |||| |||||||| ||||||||||| |||||||| || || |||||  |||| ||||| ||||| |||||||| |
------ccttccctagacccca-cccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: AT3G15980.5 (Arabidopsis thaliana), 3'ss of exon 11
----------agaagtgagtt--ttaaaacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatt----tgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
          |   || | |   | | || |||    ||   |      | || |  ||| | | |       |    |  || |||       || ||  |    |      ||||  || |||||||| || |||||||||||||| || || || || ||||| |||||||| || |||||||| ||||| ||||||                
atttgaaatgaagcgttaatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagCTATTCTAACTCTCAGAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGA----------------

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgttt-------catgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
  |||||    | |||   || |    ||| |||    |   | |  | ||||| | | |       | ||    ||| || ||   ||  |    |||     ||||  || |||||||| || |||||||||||||| || || ||||| || || || || || || ||||| || ||||| ||||||||||||||||||||||
--aagtg--cctcaaagttatggg---tatcgctaagccgcgtcttcagaatatatatctgttctcacttgatctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
--agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtt-tcatgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
  |   ||     | | ||  ||   | | | |  |   | |||| |    | ||     | ||||   || |    |||| || | ||  ||  || | ||||  || |||||||| || ||||| |||||||| || || ||||||||||||||||| ||||| |||||||| ||||| ||| |||||||||||||||| |
ttactggtattagtaagaaatatgaccttaaatcatttattaatt-ttgtgactacccactgtcatttatgtt--tctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatt----tgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
   | |   |  |||||    |   ||  ||  |   | || |  ||| | | |       |    |  || |||       || ||  |    |      ||||  || |||||||| || |||||||||||||| || || || || ||||| |||||||| || |||||||| ||||| ||||||||||| || ||||| |
--taatagatgataaaaatgaaactctgtttcata--tgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
agaagtgagttttaa--aacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
 | | | || |   |  ||  || ||    |       || | ||||    | |  |  || |||   |     | | || ||  |||  |||||  | ||||   |||| || || ||||||||||||||||||||||| |||||||||||||||||||||||||| || || ||||||||||| |||||||| |||||||
-gcattaagctaggatgaatgattgtttccaccatattttaatttattgttatttatgtttacatttatttcttccttttttttttttt-tttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT

upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
agaagtgagttttaaaacaatagtccttat------tgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
   | |   | |  ||     ||| | ||       ||| || ||| || |      |  |    | |||| |  |||||| |||||  |||  |||    | |||| ||| ||||||||| | ||||| |||| ||||||||| ||||| ||||| || ||||| ||||||||  | ||||||||||||||||| |||||||| |
---actttttctctaagaggcagtgcatagaatatgtgcgggctcagttttt--ttgttgtcacattatggttaatgactt-ttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT

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|9987279|gb|BE661387.1|BE661387
EST:     GTTACCTTTAGCTGGTAAGGAGTTTGGGTACCTGCGATCTCTACCCTCAA                         AATTTAAAAGCACAATCCAAATGGGAAGGTT-GTTG
genomic: GTTACCTTTAGCTGTTAAGGAGTT-GGGTACCTGCGATCTCTACCCTCAAgtgagttaat ... tgttgtgcagAATTTAAA-GCACAATCCAAATGGGA-GGTTTGTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacaatatttgtttcatgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
                                     atttaat  putative branch site (score: 4)
                            ttattgttgatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - -aaaacaa
- - - - - - - - - - - - - - - tgctggt
- - - - - - - - - - - - - - - - - - - - - -atcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat