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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatttttttacatattcactgtttttttatcattttttttaaattgataggttccttaattcttctttttcagtgaagagtcccccattcttttatctcactgacatgttgtttacttgtcttcaattcttcatgtgaacagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAGCCTAACTATGAG

Basic information

species Glycine max
transcript GLYMA13G31550.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 9
gtatatatttttttacatattcactgtttttttatcattttttttaaattgataggttccttaattcttctttttcagtgaagagtcccccattcttttatctcactgacatgttgtttacttg-tcttcaatt-cttcatgtgaacagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAGCCTAACTATGAG
                                                             ||  | |||| ||  |     |  |   |  |   |  || |     |  |    || |   | ||||  |||  | | ||  ||||| |||| |||||||| |||||||| |||||||||||||  || || ||  | |||||||| || 
------------------------------------------------------------gtatgttttctattgaaacctcgctttgacactgtctagatgtactcaaggttcctttcatgagctcttgtattgttccttgccaacagCATGGACGTCCACTCTATGGAGACGTTTTTGGTGTTCTGCAGCAGGACGAACCTAACTACGAT

upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 10
lower sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 10
gtatatatttttttacatattcactgtttttttatcattttttttaaattgataggttccttaattcttctttttcagtgaagagtcccccattcttttatctcactgacatgttgtttacttgtcttcaattcttcatgtga-acagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAGCCTAACTATGAG
                               | | |||||||||| |            ||  |||||||||||| | |          | || |  |   || |||    | || ||| |  ||  | | |  ||  ||| | | |||||||||||||| |||||||||||||||||||||| || |||||||||||||||||||| |||
------------------------------gtaagcattttttttta-----------tctacattcttcttttttatta------tttctatgccatctactaact--tttatttttttcccgttctta-tcgtttgtgttacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAACAAGATCAGCCTAACTACGAG

upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 2
gtatatatttttttacatattcactgtttttttatcattttttttaaattgataggttccttaattcttcttttt-cagtgaagagtcccccattcttttatctcactgacatgttgtttacttgtcttcaattcttcatgtgaacagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAGCCTAACTATGAG
                              |   | | |||  | |  | ||    |   || |  ||| |||||  | ||||   ||  | ||  || | |       | ||  || ||| ||   ||   | |||| | | || |||||||||| ||| ||||||||||||||||||||||||| |||||||| || || |||||||||
-----------------------------gtgagttactttcatcatgtagactaatctatttacccttttttttgtactgaaatatcatctatcattattttc-----agattctgattattttattt--gtacttcgt-taaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG

upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 10
lower sequence: PP1S505_13V6.1 (Physcomitrella patens), 3'ss of exon 10
gtatatatttttttacatattcactgtttttttatcattttttttaaattgataggttccttaattcttctttttcagtgaagagtcccccattcttttatctc---actgacatgttgtttacttgtcttcaattcttcatgtgaacagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAGCCTAACTATGAG
                                                |   |  | |    ||| |   | | | | |  |   ||  | |||  | ||       | ||  || |||||||      |   || ||    |    ||||||||||| ||  ||||||||||||| ||||||||||| ||    || |    || || ||||
------------------------------------------------tgagtctggttggcaatacagttgtgtta-tagattttcatctatttctatacgctgaaattgggatcttgtttaaccaattagtat-ctgtggggctgcagTATGGGCGACCCTTGTATGGAGATGTATTTGGTGTTCAGCACGTGGAGCTTGATACCTTTGAG

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|24136279|gb|BU926789.1|BU926789
EST:     CTAGCTTTGGTTATCATCCTGGTGGATGGGGCAAGCCTCCTGTTGATGAA                         TATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAG
genomic: CTAGCTTTGGTTATCATCCTGGTGGATGGGGCAAGCCTCCTGTTGATGAAgtatatattt ... atgtgaacagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttttatctcactgacatgttgtttacttgtcttcaattcttcatgtgaacagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAGCCTAACTATGAG
           cactgac  putative branch site (score: 2)
                                       ttcttcat  putative PPT
                     ttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatttttttacatattcactgtttttttatcattttttttaaattgataggttccttaattcttctttttcagtgaagagtcccccattcttttatctcactgacatgttgtttacttgtcttcaattcttcatgtgaacagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAGCCTAACTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA