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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatacacattaaaacggataacagatgtactcattgctctctagatattagtcataatttattcctgatacgactgaacttgagttttcaacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA

Basic information

species Glycine max
transcript GLYMA15G42300.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
---------tgatacacattaaaacggataacagatgtactcattgctctctagatattagtcataatttattcctgatacgactgaacttgagttttcaacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA
           | |   || || |   ||  |   | || | |  ||||  |   | ||| |   |  | |||   | || ||   ||    |   ||||    |  |||| ||||| |||||||| ||||||||||| ||||| ||||| ||||||||| ||| |||  || |||| |    
gtaatgctactagattgatcaataattattgctcctttaattacggctccttcagt-ttacttccatctcattg--gctaagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
tgatacacattaaaacggataacagatgtactcattgctctctagatattagtcataatttattcctgatacgactgaacttgagttttcaacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA
              |  |  |  |||| |  ||||   |       | |||     |  |||||   | ||  |    ||   | | | ||    |  |||| ||||| |||||||| ||||||||||| ||||||||||| || |||||| ||| |||  || |||| |    
------------gtaatgccactagat-tgatcatgattgctaccgttttatgtccatcttattg--gctaaaaagtgacaacattgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
-tgatacacattaaaacggataacagatgtactcattgctctctagatattagtcataatttattcctgatacgactg--aacttgagttttcaacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA
 | ||        | |  ||| |||     | |  |  |||  | | | | || |   | |  ||    | || |||     |    ||||||        |||| || || || ||||||||||||||||| |||||||||||  | |||||| ||| ||| ||| |||| | |  
gtaatgtggtaccagattgatcaca-----atttttcactcctttggtttcagcct--actggttatgaacaccactctttgcccatgttttct------cagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

upper sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 17
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
tgatacacattaaaacggataacagatgtactcattgctctctaga--tattag---tcataatttattcctgatacgactgaacttgagttttcaacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA
                   ||  |  | ||||||||  | ||  |   ||  ||   |  | |||| |  ||| |   |   | |||||  || |   |    |||| || || || ||||| || |||||||| || || |||||||| |||||||||||||||||||| || | || 
------------------gtactacttatactcattcatttcatgtgctaccagattttctgattt-tctctggttttatgaatcttgaaattgc--tgtatcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG

upper sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
tgatacacattaaaacggataacaga--tgtactcattgctctctagatattagtcataatt-tattcctgata-cgactgaacttgagttttcaacgg--tgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA
       |   || | |  ||  |||  | |    | |   || | | | | ||| |||  | |     | | |  || ||   ||| | |||        ||||||||||||| |||||||| ||||| ||||| |||||||| ||  | |||||| | | |||| ||   || | |  
-----ttctgcaacatgcctactagaattctgtaaaataaactttggct-tcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG

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|10847452|gb|BF070139.1|BF070139
EST:     TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtagtgttta ... aacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
EST: gi|192324528|gb|FK016449.1|FK016449
EST:     GTCTAAAATAAAAGAGGTTTGTACCTCCCATCCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
genomic: GTCTAAAATAAAAGAGG-TTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtagtgttta ... aacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
EST: gi|254349123|gb|GR860395.1|GR860395
EST:     TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtagtgttta ... aacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
EST: gi|15813913|gb|BI786188.1|BI786188
EST:     TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtagtgttta ... aacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
EST: gi|254349122|gb|GR860394.1|GR860394
EST:     TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtagtgttta ... aacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
EST: gi|6666249|gb|AW277708.1|AW277708
EST:     GGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
genomic: GGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtagtgttta ... aacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
EST: gi|17020863|gb|BM091897.1|BM091897
EST:     TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtagtgttta ... aacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
EST: gi|15815591|gb|BI787866.1|BI787866
EST:     TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
genomic: TGTCTAAAATAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtagtgttta ... aacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
EST: gi|7795790|gb|AW781187.1|AW781187
EST:     AGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
genomic: AGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtagtgttta ... aacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
EST: gi|213598475|gb|DB975934.1|DB975934
EST:     TAAAAGAGGTTGTGCCTCCCATTTTTACCAAGTTAGGCAAG                         GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC
genomic: TAAAAGAGGTTGTGCCTCCCATTCTTACCAAGTTAGGCAAGgtagtgttta ... aacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattagtcataatttattcctgatacgactgaacttgagttttcaacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA
                  tcctgat  putative branch site (score: 3)
     agtcataatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatacacattaaaacggataacagatgtactcattgctctctagatattagtcataatttattcctgatacgactgaacttgagttttcaacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- atacaca
- - - - - - - - - - - - - - - - - -tgctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgaac