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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtatttgtcctgttcatgattttgtactgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA

Basic information

species Glycine max
transcript GLYMA07G39940.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G112672_T01 (Zea mays), 3'ss of exon 3
atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtat----ttgtcctgttcatgattttgt-actgtc--tgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA
     | |    |||  |  ||| |  || | | | | |  ||      ||  | ||  | || ||||    ||||  || |       |||| | |||   || |||| |||||||| ||||||||||| ||||||||||| ||||  |||||||| ||||| || || ||||| || |||||||||||||| ||  | ||||| |
-----tgtccaatgaaaaatagtcaagtg-agatcctgtggatgcttacttt-ctttccagttagtatgacattgtattgctataaccattgtcattgttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA

upper sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtatttgtcctgttcatgat--tttgtactgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA
 | |  |  |  |   | || |  | |||     |    |  | ||   ||       ||  |   | |  || ||| | | ||  |   |      || |||| ||||| |||||||| |||||||||||||| ||  | |  |||||||| ||||| ||||||||||| || |||||||| ||||| ||  ||||||| |
-tgtagaaaaattagctgcacgaaaattgtgggtccctgatct-tgcttttggttactgatataaaagtaatcatgtccctaatattccttgtcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA

upper sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 4
atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttaga-atttgtatttgtcctgttcatgattttgtactgtc---tgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA
   |  |  |  |   | ||    | |||   | | |  |  | ||   ||       || ||     | | || ||| | | || || |  ||||   ||||||| ||||| || ||||| |||||||||| ||| ||  | |  |||||||| ||||| ||||||||||| || |||||||| ||||| ||  ||||||| |
---tagaaaaattagctgcacaaaaattgtggatccttgatct-tgcttttggttactgatataaaagtatatcatgtccctaatattttcttgtccattgtagGTATTTGATTTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA

upper sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtatttgtcctgttcatgatttt---gtactgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA
                   | |||  |    |    |  | | |    |||| || |       |    | |       || | ||    ||||       |||| || || |||||||| |||||||| ||||| ||||| |  ||||| |||||||| ||||||||||||||||||||||| ||||| || || || || |
-----------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagtaccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA

upper sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
-----atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtatttgtcctgttcatgattttgtactgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA
      | | | |  ||  |||| ||||    |  |  || | |   |    | | ||  ||||||    |  |       |   ||||||||     | | ||||| || || ||||||||||||||||||||||| ||||| |  ||||| || ||||| ||||||||||| |||||||| || ||||| || || ||||| |
gtaatgtttctttcttcacattataagtgttcttaaacccatttttgt-caagatcaagtttagaagaaatgctgaa---atatgtgattttg-----tttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA

upper sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtatttgtcctgttcatgatttt---gtactgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA
                   | |||  |    |    |  | | |    |||| || |       |    | |       || | ||    ||||       |||| || || |||||||| |||||||| ||||| ||||| |  ||||| |||||||| ||||||||||||||||||||||| ||||| |            
-----------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagTACCAATCACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------

upper sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 3
atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtatttgtcctgttcatgattttgtactg--tctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA
|| ||  |    |  ||      ||||    |  |   |   |      | |  |  |  |  | ||||  | |  || |||  | | | |      ||||||| |||||||||||||| |||||||||||||| ||||| ||||||||||||||||| ||||| |||||||||||||||||||||||||| ||||| || |
atgttccttcattagttggcttgtagtcttctttca-gttttttcaaaatgagtccaaataaat-tattcctacaatttatgcctctattcaaatcttgtagGTATTTGACTTGTTTGACACAAAGCACAATGGAATACTAGATTTTGAAGAGTTTGCGCGTGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACA

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|298196422|gb|HO041165.1|HO041165
EST:     AGTTGGCATTGTTCAAGACGAACCAGAAAGAGAGCTTATTTGCAGATAGG                         GTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAG
genomic: AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaa ... ctgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAG
EST: gi|151404635|gb|EV274449.1|EV274449
EST:     AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGG                         GTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAG
genomic: AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaa ... ctgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAG
EST: gi|192304195|gb|FG993507.1|FG993507
EST:     AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGG                         GTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAG
genomic: AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaa ... ctgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAG
EST: gi|9259434|gb|BE347581.1|BE347581
EST:     AGTTGCCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGG                         GTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAG
genomic: AGTTGGCATTGTTCAAGACGAACAAGAAAGAGAGCTTATTTGCAGATAGGgtacatagaa ... ctgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggttaaccttagaatttgtatttgtcctgttcatgattttgtactgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA
  ggttaac  putative branch site (score: 3)
          ttagaatttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtatttgtcctgttcatgattttgtactgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA

- - - - - - - - - - - - - - gcatacc
- - - - - - - - - - - - - - - - - - - - - - tggggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcatga