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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcttaccttctctttttccttccttcaattactaaatagatagataagcttcttagttcttatttatgaacaaacacaattcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCCACTGGAAGTGATAATGGAAAGCGAGCCAAACAGTATATGGAGAAGGGAC

Basic information

species Glycine max
transcript GLYMA09G36900.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G36900.4 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g01770.2 (Oryza sativa), 3'ss of exon 2
-----gttagcttaccttctc--tttttccttccttcaattactaaatagatagataagcttcttagttcttatttatgaacaaacacaattcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCCACTGGAAGTGATAATGGAAAGCGAGCCAAACAGTATATGGAGAAGGGAC
      | |  |||  || |   |  |||| |       ||   | |   |||||   | ||  |   |  | || |  ||         |  |  ||||||| ||| |||| || ||| ||||||||||||| || ||||||||||||||  | || ||||| ||||| |||||||| ||  | | |||||||||||| |
aggtaatgaagttaaattgttaatagttccgtaaacatcttttgagaatcatagactggttttcttcattgtgttaagtaatgggtggtgta-atttgcagTATGGTCTGGTGCACATTTCTGCTGGAGATTTGCTAAGGGCAGAAATTGCTGCAGGCAGTGAGAATGGGAAGCGAGCTAAGGAATTTATGGAGAAGGGTC

upper sequence: GLYMA09G36900.4 (Glycine max), 3'ss of exon 2
lower sequence: AT5G47840.1 (Arabidopsis thaliana), 3'ss of exon 2
-----gttagcttaccttctctttttccttccttcaat-tactaaatagatagataagcttcttagttcttatttatgaacaaacacaattcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCCACTGGAAGTGATAATGGAAAGCGAGCCAAACAGTATATGGAGAAGGGAC
     |  ||  | | | || |||    |  |||   |  |  | ||      || |            ||    ||   |        ||   |||||||| |||||||| |||||  ||||||||||||| || ||||| ||||| ||  |||||||||| |||||||  || || ||| |  |||||||||| ||||
tccatggaagacttcatactttttaagttctctttgctgcatgagattttctcatgaaacagaagcagattgaaaattttcctcttttgttggtatgcagTATGGTTTGGTGCATATCTCTGCTGGAGATTTGCTGAGGGCTGAAATCGCTTCTGGAAGTGAAAATGGAAGACGTGCTAAAGAACATATGGAGAAAGGAC

upper sequence: GLYMA09G36900.4 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g01280.t01 (Vitis vinifera), 3'ss of exon 3
----gttagcttaccttctctttttccttccttcaattactaaatagatagataagcttcttagttcttatttat-gaacaaacacaattc---aaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCCACTGGAAGTGATAATGGAAAGCGAGCCAAACAGTATATGGAGAAGGGAC
      | || ||  ||       |   | | | |||| || | | |    ||   ||  | |      |   || |||  ||  ||       | |||||| | | |||||| ||||||||||||||||||||| | ||||||||| ||||  |||| ||||| ||||| | |||||| ||  |||  ||||| || ||  
tattacttgcataagttactggcattactgcataaatttctcatttg--gaattgcctcgtgaagaaaaacagattgaatcaagtcatcctcgtatatgcagCATGATTTGGTGCATATTGCTGCTGGAGATTTATTGAGGGCAGAAGTTGCAGCTGGTAGTGAAAATGGGAGGCGAGCGAAGGAGTTCATGGAAAAAGGGA

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|151395853|gb|EV265730.1|EV265730
EST:     GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAG                         TACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
genomic: GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAGgttagcttac ... tcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
EST: gi|6481792|gb|AW201063.1|AW201063
EST:     NNGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAG                         TACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
genomic: GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAGgttagcttac ... tcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
EST: gi|209729403|gb|BW663678.1|BW663678
EST:     GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAG                         TACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
genomic: GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAGgttagcttac ... tcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
EST: gi|208137948|gb|GD938472.1|GD938472
EST:     GGGCTCCCGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAG                         TACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
genomic: GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAGgttagcttac ... tcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
EST: gi|17962791|gb|BM269548.1|BM269548
EST:     GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAG                         TACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
genomic: GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAGgttagcttac ... tcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
EST: gi|7232845|gb|AW568197.1|AW568197
EST:     GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAG                         TACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
genomic: GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAGgttagcttac ... tcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
EST: gi|17402194|gb|BM178976.1|BM178976
EST:     GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAG                         TACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
genomic: GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAGgttagcttac ... tcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
EST: gi|151412849|gb|EV282661.1|EV282661
EST:     GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAG                         TACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
genomic: GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAGgttagcttac ... tcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
EST: gi|151406681|gb|EV276496.1|EV276496
EST:     GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAG                         TACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC
genomic: GGGCTCCTGCTTCTGGTAAAGGAACCCAGTGCCACCTCATCACCAACAAGgttagcttac ... tcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagatagataagcttcttagttcttatttatgaacaaacacaattcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCCACTGGAAGTGATAATGGAAAGCGAGCCAAACAGTATATGGAGAAGGGAC
                 ttagttcttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcttaccttctctttttccttccttcaattactaaatagatagataagcttcttagttcttatttatgaacaaacacaattcaaatgcagTACGGTTTGGTTCATATTGCTGCTGGAGATTTACTTAGGGCAGAAATTGCCACTGGAAGTGATAATGGAAAGCGAGCCAAACAGTATATGGAGAAGGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA