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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA

Basic information

species Glycine max
transcript GLYMA07G38050.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
-----------------------------gtttgatgtgtgttgatttgccaaatgaagcttga------atttagttttccattaag---atatcaag----ggtctg-----tctgatttgtgtactttgatttatggtttg--cagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
                             | || ||   |  | | ||   | || || ||| |      |  || |||   ||   |   ||    ||    |  |||     | |    ||   | | | ||| |  ||     ||||||||||||||||||| || || |||||||| || ||||| || ||||| ||||| ||||| || |||| ||| || ||||||||||| |||||||| ||
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA

upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 21
---------------------------------------------------------------gtttgatgtgt-gttgatttg---ccaaatgaagcttgaatttagttttccattaag--------atatcaagggtctgtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
                                                               | |   | |||  || | |||   |||| | | |  |   ||   |  |    | ||        | ||  |   ||||| |    |   ||   ||   |     |  ||||||||||  || ||||||| |||||||| | ||| || ||||| |||| |||||| |||||||| ||||||||||||||||| ||| | |||||||| ||
gtatattttgtaaccttttctcttactgtttgtattccctactgatgacctatttaatgtgtagctgactttgttattaacttgtaaccaagtaatggattgcttacatgctgagctgagtaatggtcagatacaaaatctgttttgactaaatatgatgtcctcatcctatcagATTATGACCGAGTTATTAAGAACATTGAGAAAGGAGAAGCAAGGATATACCGGAAGGATGAGATTATGAAAGCTATTGGGAAAAAGCTAGACCGCTATAA

upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccat-taagatatcaagggt------ctgtctgatttgtgtactttgatttatggtttgc-agATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
  ||      | || |||    ||| | | || |  |  | |||| |||     | |||||   |      ||| | ||||| |||  ||||||   || |   | |||||||||||||||||| ||||| |||||||| ||||| |||||||||||||| || |||||||| ||||| ||||||||||||||||| |||||||||||
--ttataacattttaatt----aaaagcaact-gtttgcaattttgcatactgaagatcaaacttttcatactgacagattt-tgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA

upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
-gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatt-tgtgtactttgatttatg-gtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
    | || | | ||  ||    |||  ||   |     ||  |    || ||  | || |    |||   |||| ||| |  ||||||   ||      ||||||||||||||||||| ||||| |||||||| ||||| ||||| |||||||| || |||||||| ||||| ||||||||||||||| | |||||||||||
accattatattttttttttaataaaagcaactgtttgcata-ctgaagatcaaactttccata--ctgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA

upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
gtttgatgtgtgttgatttgccaaatgaagct--tgaat-ttagttttccattaagat---------atcaagggtctg-tctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
  ||  |     ||   |||  || | ||| |  ||| | || |   | |   ||  |         |||    ||  | ||||  |  |||  |    | ||    ||| |||||| || ||||| || || || ||||| |||||||| |||||||| ||  |||||||||| |||||||||||||||||||||||  |||| ||||||| 
-gttagta-actttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG

upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 21
------------------gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
                     | |  | ||  |  ||   | |||   ||      |   |  |    || | | |    |         ||| |   ||||   |     | || ||| ||||||||||| ||||| |||||||| || || |||||||| || ||  ||||||| || |||||||| || || ||||||||  |||| ||||||| 
gtaagtaacacctttcaatgctaagttatgcagtgtttttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG

upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 21
gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtct-gtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
| ||||| | |  | |  |||    |  | | |  |||| ||||| ||| || ||    |   | | ||||| |||      ||  ||  |   | | ||||||||||||| || || || |||||||||||||| ||||| ||||| ||  |||||||||||||||||||||| ||||||||||||||||| ||||||||
ggttgatatattgtcagatgcatcttacaacatccattt-gtttttcatcaaaatggtgattttttcgtctgcttttaaccattaaatacaatttctccagATTATGATAGGATCATCAAGAACATTGAAAGAGGAGAGGCTAGAATTTCTAGGAAAGATGAGATCATGAAAGCAATTGGGAAGAAGTTGGATCGCTACAA

upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 21
gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatttgtgtactttgat-ttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
                                     | || ||| | ||      |||||   |    || ||    |  |||| |  | |  |||  ||| || || |||||| |   |  ||||||| | ||||||||  | ||  |  | |||||||| ||||||| | |||||||||||||| ||||||| |||||
------------------------------------gtaagcttttccttg-----tcaagaaacatattgtttaagctgttttgctgctgtaattt--agACTACGACAGAATTTTGCGAGCCATTGAACGCGGGGAGGCTCGCATCGCAAGAAAAGATGAAATCATGAGAACTATTGGGAAGAAGCTGGACCGATACAA

upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 21
gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatttgtgtactttgat-ttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
                                     | || ||| | ||      |||||   |    || ||    |  | || |  | |  |||  ||| || || |||||| |   |  ||||||| | ||||||||  | ||  |  | |||||||| ||||||| | |||||||||||||| ||||||| |||||
------------------------------------gtaagcttttccttg-----tcaagaaacatattgtttaagctgttctgctactgtaattt--agACTACGACAGAATTTTGCGAGCCATTGAACGCGGGGAGGCTCGCATCGCAAGAAAAGATGAAATCATGAGAACTATTGGGAAGAAGCTGGACCGATACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattaagatatcaagggtctgtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
                                    tttgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - tgtgtgt
- - - - - - - - - tgccaaa
- - - - - - - - - - - - - - -gcttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtac