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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcttatatattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtcatgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG

Basic information

species Glycine max
transcript GLYMA11G05340.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 4
--ggcttata-tattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtcatgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
  |  |||||  |   | ||||   |   | || ||  |   ||||  || ||  ||  | ||    ||     || ||        |  |||  ||   ||||||||| || ||||||||| | || ||||| || |||   ||||||||||| ||||||||||||||||||||||| |||||||||||||||
cagtgttatagcaaatttattggttttagaagactatata-agttttcttatatttgaaaatg--tggatagttttatctgcaaacttattttctttatccagATACTTCAAAGGGCCTGAATTGCTGGTTGACTTCCAAAGTTATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATG

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 4
ggcttatatattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgac-cagacgcaattgtcatgtgctatgctt------ttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
      | |  | |  || | || |  | | |   | | ||    |   | ||  ||   |  ||||     | || | ||   | | |       ||||| |||||||||||||||||||| |||||||| |||||||||||||| ||||| || || || || |||||||||||||| ||||||||||| ||||||
------tgtggttttctt-tgatttctgaaatttttatagtaagatgggagatcctaagaattcagattttttcgtaaggtttgaagttcctttccttgttactcagATACTTTAAGGGGCCAGAACTTCTTGTTGATTTGCAAGATTATGATTATTCTTTGGATATGTGGAGCCTTGGTTGCATGTTTGCGGGAATG

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 4
ggcttatatattatgattgtaat--gtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtcatgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
   || ||||  ||     | ||  ||  | || |         |   | || | |  | |  | ||  |   ||   || |||        |||    ||||||||||||||||||||||||||| ||||||||||||||||||||||| || || || ||||||||||| || || |||||||| ||||||
attttctatagcatagacttgatttgtttgtataaatatcttgcttgctgtataggcaattttctag--gatgttaatatttgcatgttccctgtaatccagATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATG

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 4
ggcttatatattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtc-atgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
                       ||  |||  |   || |       || ||||| |     ||    ||||  |   |||||| |   ||      |||||||||| || || || || || || || ||  |||| ||||| || |||||  | |||||||||||||| ||||||||||| |||||||||
-----------------------gtgtggaaaaggcgttgc------ttgaatgtgatc--tcaattccaataatttgtgtgctgtcgcttctcacgtcagATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ28543 (Selaginella moellendorffii), 3'ss of exon 4
ggcttatatattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtc-atgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
                       ||  |||  |   || |       || ||||| |     ||    ||||  |   |||||| |   ||      |||||||||| || || || || || || || ||  |||| ||||| || |||||  | |||||||||||||| ||||||||||| |||||||||
-----------------------gtgtggaaaaggcgttgc------ttgaatgtgatc--tcaattccaatcatttgtgtgctgttgcttctcacgtcagATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG

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|207689746|gb|GD670949.1|GD670949
EST:     CTGGAAAGGAATATAATGTCCGTGTGGCTTCAAG                         ATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
genomic: CTGGAAAGGAATATAATGTCCGTGTGGCTTCAAGgtactgttct ... tgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
EST: gi|10233590|gb|BE802478.1|BE802478
EST:     GCTGAATTTTATCATCCTGGAAAGGAATATAATGTTCGTGTGGCTTCAAG                         ATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATATAATGTCCGTGTGGCTTCAAGgtactgttct ... tgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
EST: gi|38193563|gb|CF922769.1|CF922769
EST:     GCTGAATTTTATCATCCTGGAAAGGAATATAATGTCCGTGTGGCTTCAAG                         ATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATATAATGTCCGTGTGGCTTCAAGgtactgttct ... tgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
EST: gi|20813341|gb|BQ297819.1|BQ297819
EST:     GCTGAATTTTATCATCCTGGAAAGGAATATAATGTTCGTGTGGCTTCAAG                         ATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATATAATGTCCGTGTGGCTTCAAGgtactgttct ... tgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
EST: gi|214009784|gb|DB986911.1|DB986911
EST:     CTGAATTTTATCAAT-CAAGAAAGGAATATAATGTCCGTGTGGCTTCAAG                         ATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
genomic: CTGAATTTTATC-ATCCTGGAAAGGAATATAATGTCCGTGTGGCTTCAAGgtactgttct ... tgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaaatgttactgaccagacgcaattgtcatgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
          tactgac  putative branch site (score: 1)
                                       tgcttttgtttctc  putative PPT
                                          ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcttatatattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtcatgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - acctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgct