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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtgattactttctctccctggttttccctctttttccataatcattgcttattaattcagatatgtctgtatatctctcattatactttttgaaacagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG

Basic information

species Glycine max
transcript GLYMA19G41130.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41130.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 17
gtattgtgattactttctctccctggttttccctctttttccataatcattgcttattaattcagatatgtctgtatatctctcattatactttttgaaacagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG
     ||   || ||  |||       ||| | ||||  |   |  |    | |    ||| || ||      || ||    |||  |     | ||   |||||| | |||||||||  | || || ||||||||  | || || |||||||| |||||||||||||||||||||||||||||||| ||||||||||| |||
-----gtacctatttattcttagaacatttgcatcttgctgactttttgaag-tgggaaatgcaaatg-----gtgtaatattcaaaaactaatgtg---cagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCTGGGAATGGGCTATGCTACTGAAGCACTTCATTTACCTGGAATATCAAAG

upper sequence: GLYMA19G41130.2 (Glycine max), 3'ss of exon 13
lower sequence: AT5G24710.1 (Arabidopsis thaliana), 3'ss of exon 17
gtattgtgattactttctctccctggttttccctctttttccataatcat-tgcttattaattcagatatgt--ctgtatatctctcattatactttttgaa-acagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG
                         || |       |||  |||||||   || ||||      || || ||  ||| |   ||   |  | | |||||     |||||||||||| ||||| |||||||| ||||| ||| | ||||| ||||||||||| ||||| || || || ||||| ||||||||||||||||||||||||
-------------------------gtatggatatgtttctcataatctcgtgtttatgtgagtagttaagtagctggaatccttatacaacattttttttgcgcagGGCAAGTAGGCTTGGGAGAGAACATCATGACGATCTGGCACAGTTTATGCTAGGGATGGGATACGCAACAGAAGCTCTTCATTTGCCTGGAATATCTAAG

upper sequence: GLYMA19G41130.2 (Glycine max), 3'ss of exon 13
lower sequence: EFJ13686 (Selaginella moellendorffii), 3'ss of exon 17
gtattgtgattactttctctccctggttttccctctttttccataatcattgcttattaattca-gata-tgtctgtatatctctcattatactttttgaaacagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG
                                                  | | | ||  | || |||| |   |   |  |   |||| ||  |||     ||||||    || |||||| |||| |||||||| ||  | || |||||||||||||| ||||| ||||||||||||||  | ||| |||| || || || |||
-------------------------------------------------gtacgtttttctgcatgatagtacttactttaccggcattttatgttt----gcagGGCTTTCAGGCTTGGACGAGAGCACCATGACGACCTTGCTCAATTTATGCTAGGCATGGGATATGCTACTGAAGCTTTACATCTGCCGGGCATTTCGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcttattaattcagatatgtctgtatatctctcattatactttttgaaacagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG
      tattaat  putative branch site (score: 2)
                                        tacttttt  putative PPT
     ttattaattcagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtgattactttctctccctggttttccctctttttccataatcattgcttattaattcagatatgtctgtatatctctcattatactttttgaaacagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC