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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacttgattgacacctaatatttaaggaattttttttaataaggggccaagttaattccattgagtatcattataataaatttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGATATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGAGATCTTGCTGTTTTCT

Basic information

species Glycine max
transcript GLYMA06G30000.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G30000.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G318635_T01 (Zea mays), 3'ss of exon 17
gacttgattgacacctaatatttaaggaattttttttaataaggggccaagttaattccatt-----gagtatcattataataaatttagctgtggttttgc-tagGCAACTATCTATCAGCAAAAGGCACTAGATATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGAGATCTTGCTGTTTTCT
      ||   ||| |   |  |    |||||||||  | ||  |   |  |  || | ||       ||  | |   | |||||| | ||||   |||     ||||||| |||||||| || |||||  ||||||||||||| || || |||||||| ||||| || ||||| |||||||| ||||||||||||||||||||||
------atatgcacttgtcaggtgtttaatttttttccacaacagcgtagttctatcctatgctgtgaaggcttaactttataaatgttgctgctctttcaaacagGCAACCATCTATCAACAGAAGGCTTTAGATATTAATGAGAGGGAACTTGGACTTGACCACCCAGATACAATGAAAAGCTATGGAGATCTTGCTGTTTTCT

upper sequence: GLYMA06G30000.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv11s0037g00840.t01 (Vitis vinifera), 3'ss of exon 17
gacttgatt----gacacctaatatttaaggaattttttttaataaggggccaagttaattccattgagtatcattataataaatttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGATATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGAGATCTTGCTGTTTTCT
 |||| |||    || |   | | |    ||| ||| | ||  | |      |  || |    |    || ||||  || |     ||  | |  ||||  |||||||| |||||||||||||| ||  | ||||| ||||| |||||||||||||| || ||||||||||| |||||||||||||| ||||||||||||||||
cacttcatttgaagaaagacattgtcctgggattttctatt--tgaaaaataatattcacattaaattgtttcatattattggccctatttat--ttttcgtagGCAACCATCTATCAGCAAAAAGCTTTGGATATCAATGAGAGAGAGCTTGGACTTGATCATCCTGATACAATGAAAAGTTATGGGGATCTTGCTGTTTTCT

upper sequence: GLYMA06G30000.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
gacttgattgacacctaatatttaaggaattttttttaataaggggccaagttaattccattgagtatcattataataaatttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGATATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGAGATCTTGCTGTTTTCT
                             |       |   |         |||||   |||||  |      | || | |||   |||| |      |||| |  || || |||||||| ||  | || || ||||| || ||||||||||| |||||||| ||||| |||||||| ||||| ||  | ||||| || |
----------------------------gtacacaaaagctacatattgtattaatgtaattgatgacttaattgatgacttt--ttgtgatc-----agGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT

upper sequence: GLYMA06G30000.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ26734 (Selaginella moellendorffii), 3'ss of exon 17
gacttgattgacacctaatatttaaggaattttttttaataaggggccaagttaattccattgagtatcattataataaatttagctgtggtt--ttgctagGCAACTATCTATCAGCAAAAGGCACTAGATATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGAGATCTTGCTGTTTTCT
                                             | |  ||    ||  ||| |  |   || |||  |      ||| |    ||   |||| || ||||| || ||||||||  |||| || |||||| | ||||||||  |||||||||| ||||| ||||| || ||||||||||| ||||| || |
---------------------------------------------gtctggtcttgtcacttgcggttttatacaatctaaacgtttgtcgacgcttctcagGCTACCATCTACCAACAAAAGGCTTTAGACATCAATGAACGCGAGCTTGGCTTGGACCATCCGGATACCATGAAGAGCTATGGAGATCTGGCTGTCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaagttaattccattgagtatcattataataaatttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGATATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGAGATCTTGCTGTTTTCT
    agttaat  putative branch site (score: 4)
                                              ttttgct  putative PPT
              attgagtatcattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacttgattgacacctaatatttaaggaattttttttaataaggggccaagttaattccattgagtatcattataataaatttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGATATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGAGATCTTGCTGTTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - -cacctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctgtg