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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatgttgtgcttgattactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

Basic information

species Glycine max
transcript GLYMA16G25450.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6
gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatgttgtgcttgattactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
|||    |||    ||| ||  ||     | | |     | | |  ||   |   ||  |||  ||| |  |||| || ||   |   |    |   | |||||||||| |||||||||||||| |||||||||||||| || || || ||  |||||||||| ||||||||||| ||||||||||||||||||
gtaactatttcaagcttgcttgattttcatctgtg--catgtgcctaccaaatacattctgtaattg-tacctaactgtttaactcattgcactataccagGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 5
gtactgcttttgctctttctcaatccatgttt-tttgttcttttctcactgtaactatgttgtgct-tgattactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
|||    |||    |||  | |||     | | |         |  || | | | | |||     | |   ||    ||     | |  | | ||| |   |||| ||||| |||||||||||||| || ||||||||||| || || || ||  |||||||||| ||||||||||| ||||||||||||||||||
gtaactatttcaggcttgattaattttcatctgtgcaaatgcctaccattttcattctgtaagattgtacctaaatgtttaactcatttgcactatacc--agGACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatgttgtgcttgatta---ctaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
                   | |  |||   |   |    |    ||| |   | |   |||| |||| |||   |   |||   | ||||  |  ||| |  |||||||||| || ||||||||||| || || ||||||||||| || || || || |||||||| ||||| ||||| ||||| || ||||| |||
------------------gtaatgccactctagctcacatcaattcattcagattg-attgtccttgcttatatcagcttgacgcattgg--aacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT

upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatgttgtgcttgattactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
         |  || ||||  | |   |||   |||  || ||||   |  ||| || |     |   || |||| | | |         || |   | ||||||| || |||||||| ||||| |||||||||||||||||||| || ||  |||| ||||| ||||||||||| |||||||| |||||||||
--------gtaactttttcatactt-gtgtacattgacctgttct---ttgaacaatatgtacatcagttgctaagttgct--------gttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT

upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatgttgtgcttgattactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
                      | | || ||  |  |  | | |  |    | || ||      |||   |  | |   |   |||  | || |   | |||| || || |||||||| ||||| |||||||||||||| ||||| || ||  |||| ||||| ||||| ||||| |||||||| |||||||||
--------------------gtagctattttcatactcgtgtacagatctgagctttgaacaatttgtacatcagtcactaagttgc-tgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT

upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatgttgtgcttgattactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
          | |  |||||  |  | | ||   | | |     |   | |  ||   || |||||   |||||| |   | |    ||   || ||  |||||||||| |||||||| ||||| || |||||||||||||| ||||| ||| | || || |||||||| || || || | |||||||||||||
---------gtacaatttctttaaaccttttccctatccaacatttttttt--cttacttttgctta--tactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT

upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------------------gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatg-ttgtgcttga---ttactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
                                         ||  |  |  |  | | |||||||| |   ||  |||   ||| |  | | |   |   ||  |  | |    || ||||    |   ||  ||  ||  |  ||||||| || || ||||||||||| ||||| ||||||||||| ||||||||  |||| || ||||||||||| || ||| ||||||||||||||
gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcat-ttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattac-attttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT

upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
------------gtactgcttttgctctttct----caatccatgttttttgttct---tttctcactgtaactatgt---tgtgcttgatt---actaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
             |||  || |  |||| | |     |  | || | | || | ||    |||||  |||   | ||    ||| |||  ||   | | | || |   ||   |  |  | | |||||||| || ||||||||||| || ||||| |||||||| || ||||||||| |||| || || ||||||||||| |||||||| || || || 
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC

upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
lower sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------------gtactgctt--ttgctctttctcaatc-catgttttttgtt--cttttctcactgtaacta--tgttgtgcttgattactaattggttccttgggtattatgctct------agGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
                                                                           |||| | ||  |||   | |   | |  ||| ||  |   |  ||| |||   |  ||| |  |||  |    | || |  |   ||| ||     | |   ||||      |||| |||||||||||||| ||||| || || ||||| || |||||||| || ||||| |||||| | |||||| ||||||||  ||| ||||||
gtaatttcgtgcttaggcatagagtttctcagaataatgcatttcatgttgtgttagatgcaaactcgttttcaagtaccgattatttgaagtattgtagttgcattttggtcactgccttctctggattcaacaagatgtgatttgcggtttcagagatgttgctgacaaagttacctctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGT

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|13789639|gb|BG652230.1|BG652230
EST:     TATGCTCGTATTATCCAAAAGCTTGGCTTCCCAGCCAAATTTAAG                         GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
genomic: TATGCTCGTATTATCCAAAAGCTTGGCTTCCCAGCCAAATTTAAGgtactgcttt ... tatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
EST: gi|208239540|gb|GE038626.1|GE038626
EST:     TATGCTCGTATTATCCAAAAGCTTGGCTTCCCAGCCAAATTTAAG                         GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
genomic: TATGCTCGTATTATCCAAAAGCTTGGCTTCCCAGCCAAATTTAAGgtactgcttt ... tatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
EST: gi|254320724|gb|GR827173.1|GR827173
EST:     TATGCTCGTATTATCCAAAAGCTTGGCTTCCCAGCCAAATTTAAG                         GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
genomic: TATGCTCGTATTATCCAAAAGCTTGGCTTCCCAGCCAAATTTAAGgtactgcttt ... tatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
EST: gi|14258923|gb|BG881840.1|BG881840
EST:     TATGCTCGTATTATCCAAAAGCTTGGCTTCCCAGCCAAATTTAAG                         GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
genomic: TATGCTCGTATTATCCAAAAGCTTGGCTTCCCAGCCAAATTTAAGgtactgcttt ... tatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtaactatgttgtgcttgattactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
                       tactaat  putative branch site (score: 1)
                     attactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatgttgtgcttgattactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG