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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatgaagtttggttccatgtcttgatgctttcataccaaaacgaataacaataaatgatcctgaaagctcaaactgactgtacttttgtatcttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT

Basic information

species Glycine max
transcript GLYMA06G17140.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
---tgcatgaagtttggttccatgtcttgatgctttcataccaaaacgaataac-aataaatgatcctgaaagctcaaactgactgtacttttgtatcttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT
    |||  |||     | | ||  || ||||||| |  |  |  |    | |  ||| | ||   |  |||  ||    |||   | ||||  |    | |||||||||| | ||| | |||||||||||||| ||| ||||||| || |||||||| |||||||| || ||| |||| ||||||||||||||||| ||  | 
gtgagcaccaagaaca-tgcaatcactcgatgcttcctcataagcattgttgatgaattattgtaacccaaaagtcttgatgaacctgcttt-atgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G059825_T01 (Zea mays), 3'ss of exon 3
------------------tgcatgaagtttggttc-catgtcttgatgctttcataccaaaacgaataacaataaatgatcctgaaagctcaaactgactgtacttttgtatcttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT
                  | || | | |    ||  ||  ||       |||  | |    ||   |  |      |  ||    | |     |||||  | | |    | |  |||||||||||  | ||| | || ||||||||||| ||| |||| || ||||||||||| || || || || ||| ||||||||||||| |||||||| ||  | 
gtaattcatctatctgtctacaagcaatgcaattggcacctcgctcatttttggtcctcccactgcttcctgggtctattctctgatg-----actgatggcattgcc-tgttctacagAGGTGCTCGTGCATCGGTCTGGGAGAACTTCAAGAACAACCCGCTGTTTGACATCTCGACCGATCACCCACCAACATACTACGAAGACATGCAGCGCTCG

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G448834_T02 (Zea mays), 3'ss of exon 2
-tgcatgaagtttggttccatgtcttgatgctttcataccaaaacgaataacaataaatgatcctgaaagctcaaac--tgactg-tacttttgtat-cttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT
     | ||||  || |||  |||       |   || ||||  | ||||  | || ||| |  |  |     |  |  ||  || |   |    || | | ||| || ||  | ||  | |||||||||||||| |||||||| || ||||| ||||| || || ||||| ||  | || ||||||||||||||||| || || 
gcaagtcaagtc-ggctccg-gtccattccatccaatgccaatgccaata-tagtacatgtttatttatatatatgccatggttggtggatgatcatgcatgcagGGGCGCTCGCGCGTCGGTGTGGGAGAACTTCAAGGACAACCCGCTGTTCGACATCTCGACGGAGCACCCGTCGACGTACTACGAGGACATGCAGCGCGCC

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------------------------tgcatgaagttt-ggttccatgtcttgatgctttca----taccaaaacgaat----aacaataaatgatcctgaaagctcaaactgac-tgtacttttgtatct--tacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT
                                                                                     |  || | ||| ||    |   ||  |       |    || || |  |  |    | | ||  ||  | || | |        |||  | |  || |  | ||   |||| ||||| |||||||| || ||||| ||||| || |||||||| ||||||||||| || |||||||| ||||||||||| || |||||||||||  |||| 
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
tgcatgaagtttggttccatgtcttgatgctttcataccaaaacgaataacaataaatgatcctgaaagctcaaactgactgtacttttgta---tcttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT
   ||    ||| ||||| |   |||     |       || | |||    |    | |||  |      || ||||   | |  ||||| |   | || |||||| ||  | ||||| ||||||||||| ||||| ||||||||||| |||||||| || |||||||| ||||  || || || |||||||||||||| |||
---attgttttttgttccttaatttgtccaatgatctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
-------tgcatgaagtttggttccatgtcttgatgctttcataccaaaacgaataacaataaatgatcctgaaagctcaaactgactgtacttttgtatcttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT
         |||   || || | | ||| |||  | |||| |||  |   |   |     | |||||  |   ||   | | || ||| |  ||   |   | |||||||||| || |||||||| |||||||||||||||||||| || || |||||||| ||||| ||||| ||||| ||||| || || ||||||||||| |||
aggaagcaacatcttgtatgatac-atggctttgt-cttttatattaggtcctttgg-gttgaatgaatc---aactcctatctaactct-tttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
tgcatgaagtttggttccatgtcttgatgctttcataccaaaacgaataacaataaatgatcctgaaagctcaaactgactgtacttttgtatctta--cagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT
                        | | | | ||  |  | |  ||| | |  |   |||     | | || |  | |     || ||||   || |  ||| |||||  | || || || |||||||| || ||||| ||||| || |||||||| || || ||||| || |  || ||||||||||||||||| ||||||
-----------------------gtaaagttctctcaatacatagaaaagctttgtttgaa---aagatcttattcggttctgacatttgctgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT

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|208264066|gb|GE061218.1|GE061218
EST:     GGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAG                         AGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCGCTGTTTGA
genomic: GGACTGTTTTATGATGTTGGAAATGACCCCGAAGGTGGATACTATGCAAGgtatgtctta ... tatcttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataacaataaatgatcctgaaagctcaaactgactgtacttttgtatcttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT
                            aactgac  putative branch site (score: 2)
                                       cttttgt  putative PPT
      aataaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatgaagtttggttccatgtcttgatgctttcataccaaaacgaataacaataaatgatcctgaaagctcaaactgactgtacttttgtatcttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
-gcatgaa
- - - - - - - - -catgtct
- - - - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - - - -ccaaaac
- - - - - - - - - - - - - - - - - - - - - - gaataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaaac