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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatgaactaatctcatggatagaatagttaacagatctttgagtgtaaatttcttatcatctcatctcttaacccttttcctatgcattttcacctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATTGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA

Basic information

species Glycine max
transcript GLYMA13G31550.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 12
aaatgaactaatctcatggatagaatagttaacagatctttgagtgtaaatttcttatcatctcatctcttaacccttttcctatgcattttcacct--cagCACTCCCACTGGAGTGGAAACACCTGATGTTATTGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA------------
                  | ||  ||| ||    |||   | | | ||  |||  | ||  |  |      |||  | |    |||  | ||   ||   |||||||| ||||| ||||||||||||||||| ||||| || |||||||  ||| |||| |||||||| | ||      |  |             
----------------gtgctaccataattctttgatgccttact-tagtttttctttc--ccaaataaagaactatgtattgatgtttgttttgctgatagCACTCCAACTGGTGTGGAAACACCTGATGTGATTGATCTTCGGAAGCTGCAGCGGAAAGAGCCTGAAAAGCAGACCGAGAAGCAACTATACCAG

upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G132060_T02 (Zea mays), 3'ss of exon 11
-aaatgaactaatctcatggatagaatagttaacagatctttgagtgtaaatttctt--atcat-ctcatctcttaacccttt---tcctatgcattttcacct-----cagCACTCCCACTGGAGTGGAAACACCTGATGTTATTGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA------------
    |  ||||   |  |   |  | || ||   || || |||  |     ||||||   | || || ||    ||  | | |    |  |    |||| ||||     ||| ||||| ||||| || ||||||||||||||||| ||||| |||||||  |||||||||||| |||| | ||      | |              
gtggtttactatatttctttctttagtattttgtaggtccttgttttcccttttctttagtaatgctgatgcagtagacatgtatgcctaacttttttttacctccaaccagTACTCCAACTGGTGTTGAAACACCTGATGTTATCGACCTTCGGAAGCTGCAGAGGAAGGAGACTGACAAGCAGGCAGAACGGCCGCTGTACCAG

upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 7
aaatgaactaatctcatggatagaatagttaacagatctttgagtgtaaatttctt-----at-------catctcatctcttaacccttttcctatgcattttcacctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATTGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA------------
   |||  ||      |   |  | |  ||   ||    |||  | |   ||||||     ||       ||   ||  | |   |   ||  || |     | || | ||| ||||| ||||| || ||||||||||||||||| ||||| |||||||  |||||||||||| |||| | ||      | |              
--gtgatttacgtatttctctgtattgttttgtaggcacttggttttccttttctttagtaatggtgatgcagtacacatgtagcctaattctctctctgcgtccaac-cagTACTCCGACTGGTGTTGAAACACCTGATGTTATCGACCTTCGGAAGCTGCAGAGGAAGGAGACTGACAAGCAGGCAGAACGGCCGTTGTATCAG

upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 4
aaatgaactaatctcatggatagaatagttaacagatctttgagtgtaaatttcttatcatctcatctcttaacccttttcctatgcattttcacctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATTGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA
      | || |     |  | |   |||         | | |   |||    ||| | ||||    |  | | |  |||  |   |   |     ||||||| || ||||| || || |||||||||||||||||||| || |||||||||||||||||||| |||||||| |||||||||
gggaccattagtaaggagtctgggcaagtctttctgcatatcatcttaagaaacttgtaatctttattaatgatcactttttttccctcctcttattcagCACCCCAACTGGTGTTGAGACACCTGATGTTATTGACCTACGTAAGCAACAGAGGAAGGAGCCAGAGAGGCCACTTTATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaatttcttatcatctcatctcttaacccttttcctatgcattttcacctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATTGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA
                      tcttaac  putative branch site (score: 2)
                                           ttttcacctc  putative PPT
     tttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatgaactaatctcatggatagaatagttaacagatctttgagtgtaaatttcttatcatctcatctcttaacccttttcctatgcattttcacctcagCACTCCCACTGGAGTGGAAACACCTGATGTTATTGACCTCCGGAAGCAACAGAGGAAGGAGCCTGAGAGGCCTCTTTATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
-aatgaac
- - - - - - - catggat
- - - - - - - - - - - - - - - - - - - - tgagtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcatt