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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtagtcatcaaaagttgataattgatttcgactaaattatctccagattttaagcatcattgtctttgcagGTTGGAGCCTTTTCTGTTTTGAAAGAACTTGTGGTTGTATTACCCAACTGTCTTGCAGATCACATTGGGTCACTCATTCCAGGAATTGAAAAAGCATTGA

Basic information

species Glycine max
transcript GLYMA17G00570.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 12
gtagtagtcatcaaaagttgataattgatttcgactaaattatctccagattttaagcatcattgtctttgcagGTTGGAGCCTTTTCTGTTTTGAAAGAACTTGTGGTTGTATTACCCAACTGTCTTGCAGATCACATTGGGTCACTCATTCCAGGAATTGAAAAAGCATTGA
   ||   |      | |    || | || || |   |  |   ||  |||||||   |  |||       ||||||||||| || ||||| ||||| || ||||| |||||| | ||  |||||||||| ||||| |||||||||||  |||| || ||||| || || ||||
---gtgagctctttgact--gcaaatcatgtctatcgacctggttct-gattttagataaaattt------cagGTTGGAGCATTCTCTGTATTGAAGGAGCTTGTTGTTGTACTGCCAGACTGTCTTGCTGATCATATTGGGTCACTTGTTCCTGGGATTGAGAAGGCTTTGA

upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G168629_T04 (Zea mays), 3'ss of exon 12
gtagtagtcatcaaaagttg--ataattgatttcgactaaattatct-ccagattttaagcatcattgtctttgcagGTTGGAGCCTTTTCTGTTTTGAAAGAACTTGTGGTTGTATTACCCAACTGTCTTGCAGATCACATTGGGTCACTCATTCCAGGAATTGAAAAAGCATTGA
     |||| |  |   ||     |||| ||        |||| |    | |||| ||  | | |     ||| |||||||| || ||||| ||  |||| || |||||||||||||||||  |||||||||| |||||  | ||||||||  |||| || ||||| || || ||||
--gtcagtccttcagttttcctgcaattcatggttctggaattgtaagtctgattatattcctaaca--ttttccagGTTGGGGCATTTTCAGTACTGAAGGAGCTTGTGGTTGTATTACCAGACTGTCTTGCTGATCATTTCGGGTCACTTGTTCCTGGGATTGAGAAGGCTTTGA

upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G386614_T01 (Zea mays), 3'ss of exon 1
gtagtagtcatcaaaagttg--ataattgatttcgactaaattatct-ccagattttaagcatcattgtctttgcagGTTGGAGCCTTTTCTGTTTTGAAAGAACTTGTGGTTGTATTACCCAACTGTCTTGCAGATCACATTGGGTCACTCATTCCAGGAATTGAAAAAGCATTGA
     |||| |  |   ||     |||| ||        || | |    | |||| ||  | | |   | ||| |||||||| || ||||| ||  |||| || |||||||||||||||||  |||||||||| |||||  |||| |||||  |||| || ||||| || || ||||
--gtcagtccttcagttttcctgcaattcatggttctggaactgtaagtctgattatattcct-agcattttt-cagGTTGGGGCATTTTCAGTACTGAAGGAGCTTGTGGTTGTATTACCAGACTGTCTTGCTGATCATTTTGGATCACTTGTTCCTGGGATTGAGAAGGCTTTGA

upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 12
gtagtagtcatcaaaagttgataattgatttcgactaaattatctccagat---ttta-agcatcatt-gtctttgcagGTTGGAGCCTTTTCTGTTTTGAAAGAACTTGTGGTTGTATTACCCAACTGTCTTGCAGATCACATTGGGTCACTCATTCCAGGAATTGAAAAAGCATTGA
      ||    ||  ||| |  |||  ||| |  |   ||       |||   || | | | || ||  | | || |||||||||| || |||||||||| |||||||||||||||  | ||  |||||||||| ||||| ||||| |||||  |||| ||||||||||  ||  | |
------gtatgaaagtgttaaacattctttttggtttggttcctgtttgatactttcataacttctttcatatctgtagGTTGGAGCATTCTCTGTTTTGAGAGAACTTGTGGTTGTCCTGCCTGACTGTCTTGCTGATCATATTGGTTCACTTGTTCCTGGAATTGAAAGGGCGCTAA

upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 13
gtagtagtcatcaaaagttgataattgatttcgactaaattatctccagattttaagcat-cattgtctttgcagGTTGGAGCCTTTTCTGTTTTGAAAGAACTTGTGGTTGTATTACCCAACTGTCTTGCAGATCACATTGGGTCACTCATTCCAGGAATTGAAAAAGCATTGA
|||  |||   |  |  ||  |        ||    |  | | |    ||  || | ||| ||||   | |||||||||| || ||||| ||||||||||| ||||||||||| || ||  |||| || ||||| |||||||| ||||| ||| | ||||| ||||||||  | |
gtacgagtttcctgatattcttttaaaggatctgtgatgtaaccattggaaatttaacattcatttcatctgcagGTTGGTGCATTTTCAGTTTTGAAAGAGCTTGTGGTTGTCTTGCCAGACTGCCTGGCAGACCACATTGGATCACTTATTTCGGGAATCGAAAAAGCGCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataattgatttcgactaaattatctccagattttaagcatcattgtctttgcagGTTGGAGCCTTTTCTGTTTTGAAAGAACTTGTGGTTGTATTACCCAACTGTCTTGCAGATCACATTGGGTCACTCATTCCAGGAATTGAAAAAGCATTGA
             gactaaa  putative branch site (score: 2)
                                           ttgtcttt  putative PPT
              actaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtagtcatcaaaagttgataattgatttcgactaaattatctccagattttaagcatcattgtctttgcagGTTGGAGCCTTTTCTGTTTTGAAAGAACTTGTGGTTGTATTACCCAACTGTCTTGCAGATCACATTGGGTCACTCATTCCAGGAATTGAAAAAGCATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA