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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gataaggctttgttgctttaattttttctggaaattagtttctgtttagaatgtttcaaggttctgcctaattggtgcattttttaatcattgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA

Basic information

species Glycine max
transcript GLYMA13G28720.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
-------------------------------------gataaggctttgttgctttaattttttctgga-aattagtttct---gtttagaatgtt----tcaaggttctgcctaattggtgcat--tttttaatcattgtctg--cagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA
                                      ||      ||  | | | ||| ||  |   | |  || |||||   ||   ||||| |    | |    |     | |||||   ||  || ||| | | ||||    |||||||||| |||||||| || || ||||||||||| ||||| || || || ||||| ||||| || ||||  || || || |||||||| |||||||| ||
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA

upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 21
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
-gataaggctttgttgctttaattttttctggaaattagtttctgtttagaatgtttcaaggttctgcctaattggtgc-attttttaatcattgtctg--cagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA
  ||||   |||  |    |||      |||      | |||   |   |||  |   |   |||   || |  | |    | |||| ||||||||      ||||||||| |||||||| ||||| |||||||||||||| |||||||| || || || |||||||| |||||||||||||| |||||||| |||||||||||
ttataacattttaat----taaaagcaactgtttgcaattttgcatactgaagatcaaacttttcatactgacagattttgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA

upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
gataaggctttgttgctttaattttttctggaaattagtttctgtttag-aatgtttcaaggttctgc-ctaattg---gtgcattttttaatcattgtctg--cagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA
       | || |   |||  |||||  |  ||   | | | ||  ||   | | |  ||  |||    || || |   ||| || |||| ||||||||     |||||||||| |||||||| ||||| |||||||||||||| ||||| || || || || |||||||| |||||||||||||| |||||| | |||||||||||
-----accattatattttt--tttttaataaaagcaactgtttgcatactgaagatcaaactttccatactgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA

upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 21
------------------gataaggctttgttgctttaattttttctggaaattagtttctgtttagaatgtttcaaggttctgcctaattggtgcattttttaatcattgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA
                      | | | ||  |  ||  |   |  |   || || || ||   |  ||          | ||   ||| |    ||| |||   ||    | || ||| ||||| ||||| ||||| |||||||| ||||| |||||||| || ||| ||||||| || ||||||||||| || || |||||  |||| ||||||| 
gtaagtaacacctttcaatgctaagttatgcagtgtttttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG

upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 21
-gataaggctttgttgctttaattttttc-tggaaattagtttctgtttagaatgtttcaaggttctgcctaattggtgcattttttaat-cattgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA
 | | |    ||||    |  || ||         ||| |||| |  | | |||| |  |   ||  | ||  ||  |  |   || ||| || | ||| |||||||||| || || || || ||||||||||| || ||||| ||||||||| ||||||||||||||||||| || ||||| ||||||||||| ||||||||
ggttgatatattgtcagatgcatcttacaacatccatttgtttttcatcaaaatggtg-attttttcgtctgctt--ttaaccattaaatacaatttctccagATTATGATAGGATCATCAAGAACATTGAAAGAGGAGAGGCTAGAATTTCTAGGAAAGATGAGATCATGAAAGCAATTGGGAAGAAGTTGGATCGCTACAA

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|193453414|gb|FK417258.1|FK417258
EST:     AAAGATACAAGGAATTTAAATG                         ATTATGACAGAATTATTAAAAACATTGAAA-GGGGGAGGCAAGAATTTCT
genomic: AAAGATACAAGGAA-TTAAATGgtatgttaca ... ttgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCT
EST: gi|298166870|gb|HO010309.1|HO010309
EST:     GGTCTTCGAAGAAAGATACAAGGAATTAAATG                         ATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC
genomic: GGTCTTCAAAGAAAGATACAAGGAATTAAATGgtatgttaca ... ttgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaatgtttcaaggttctgcctaattggtgcattttttaatcattgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA
                                    ttttaat  putative branch site (score: 3)
                                 attttttaatcattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gataaggctttgttgctttaattttttctggaaattagtttctgtttagaatgtttcaaggttctgcctaattggtgcattttttaatcattgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - tgttgct
- - - - - - - - - - - - tttctgg
- - - - - - - - - - - - - - - - - - -gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattt