Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtactgattattcctttcaattgcggtgagctggagatggatgcgtgattgcattatgatttatgactttttgatcttagattcctgttgctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATACTGATTGATCCAAAGGCCCTTATGCATGTCATTGGAACTAAAATGGATTT

Basic information

species Glycine max
transcript GLYMA19G37930.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G37930.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g01610.1 (Oryza sativa), 3'ss of exon 2
tgtactgattat-tcctttcaattgcggtgagctggagatggatgcgtgattgcattatgatttatgactttttgatcttagattcctg-----ttgctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATACTGATTGATCCAAAGGCCCTTATGCATGTCATTGGAACTAAAATGGATTT
       || || ||| ||      |||  |  ||    |       |  |   |||||| |||      | || ||  || |   |        || ||   ||||||||||||| |||||||||||| | ||||| ||||| || ||||   |||| || ||||| ||||| || ||||||||||| || || || ||||||| 
------catcatctccattgtccaacggctacatgttcctcttcctctactgctattatgtttttatttctattcatgctaaagagcgaaatatctgtttattcagATGAAAAAGGCAAGTTTGATGAGGTTGTTGAAGATAAAGGAGTTAAAGTACTAATCGATCCCAAGGCTCTGATGCATGTCATCGGCACCAAGATGGATTA

upper sequence: GLYMA19G37930.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g30030.2 (Oryza sativa), 3'ss of exon 2
tgtactgattattcctttcaattgcggtgagctggagatggatgcgt------gattgcattatga--tttatgactttttgatcttagattcctgttgctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATACTGATTGATCCAAAGGCCCTTATGCATGTCATTGGAACTAAAATGGATTT
     | |||  |    | |||||   |  |||  | | |     ||      || |   ||||||   ||||     | |  |  |  || |   ||  ||   ||||||| || || || || |||||  | || || ||||| || |||| |||||| |||||||| || || |||||||| || |||||||| |||||||||||
-----ttatttctgtgcttaattgt--ttggctacaaacgatccagttaatctgactaatttatgaaacttatactagtattgtaatttatgctcattatttct-cagATGAGAAGGGAAAATTCGATGAACTTGTGGAAGATAAAGGAGTTAAGATACTAATTGATCCGAAAGCTCTTATGCACGTGATTGGAACCAAAATGGATTT

upper sequence: GLYMA19G37930.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g03400.t01 (Vitis vinifera), 3'ss of exon 1
tgtactgattattcc-------tttcaattgcggtgagctggagatggatgcgtgattgcattatgatttatgactttttgatcttagattcctgttgctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATACTGATTGATCCAAAGGCCCTTATGCATGTCATTGGAACTAAAATGGATTT
   | | ||||||||       |||   ||  ||  |||      | | |   | ||| || | |||   |    || || || |   ||| || ||  ||| | |||||| |||||||||||||||||||||||||||||||||||||| | |||  |||||||||||||||| || |||||||||||||| || || ||||||||
-taattaattattccaggaatctttttgttttgg-aagccattatttggtatataatttcactgtgaacaa----ttcttaatttatcattgctctt-ttttaatagATGACAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTAAAGATTTTGATTGATCCAAAGGCTCTCATGCATGTCATTGGTACAAAGATGGATTT

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|31311334|gb|CD396537.1|CD396537
EST:     AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAG                         ATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
genomic: AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAGgtctgtcact ... gctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
EST: gi|23729629|gb|BU762912.1|BU762912
EST:     AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAG                         ATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
genomic: AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAGgtctgtcact ... gctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
EST: gi|58018339|gb|CX705081.1|CX705081
EST:     AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAG                         ATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
genomic: AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAGgtctgtcact ... gctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
EST: gi|31308109|gb|CD393312.1|CD393312
EST:     AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAG                         ATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
genomic: AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAGgtctgtcact ... gctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
EST: gi|213601090|gb|DB964625.1|DB964625
EST:     AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAG                         ATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
genomic: AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAGgtctgtcact ... gctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
EST: gi|7233513|gb|AW568858.1|AW568858
EST:     AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAG                         ATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
genomic: AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAGgtctgtcact ... gctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
EST: gi|213617107|gb|DB963580.1|DB963580
EST:     AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAG                         ATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC
genomic: AGTCAAGACTCGCGGCTGTAACGGCTTATCCTACACCCTCAATTACGCAGgtctgtcact ... gctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgattgcattatgatttatgactttttgatcttagattcctgttgctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATACTGATTGATCCAAAGGCCCTTATGCATGTCATTGGAACTAAAATGGATTT
                        ttttgat  putative branch site (score: 4)
                                           ttgcttt  putative PPT
        attatgatttatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtactgattattcctttcaattgcggtgagctggagatggatgcgtgattgcattatgatttatgactttttgatcttagattcctgttgctttgacagATGAAAAAGGGAAGTTTGATGAGTTGGTTGAGGATAAGGGTGTTATGATACTGATTGATCCAAAGGCCCTTATGCATGTCATTGGAACTAAAATGGATTT

- - - - - - -cctttca
- - - - - - - - - - - tgcggtg
- - - - - - - - - - - - - - - gctggag
- - - - - - - - - - - - - - - - - - - tggatgc
- - - - - - - - - - - - - - - - - - - - - - - - - tgcatta