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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgttgatattggctctctttctctctcatacctgaatatttcagatgactgacattttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG

Basic information

species Glycine max
transcript GLYMA13G20780.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------gtatattgttgatattggctctctttctctctcatacctgaatatttcagatgactgacatt-ttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG
                                           ||  ||||   | || |      |  || |      |   | |||||  ||| ||   || |    ||  |  | |  ||  ||   ||||||| ||||| || ||| | |||||| |||||||||||||||| ||||| || |||||||| ||| | |||||||| ||||| ||||||| |||||||
gtaataaaaatgagtcttgaactgtttattttgtcagtccatcattgtgttagcactgtccactacttactgtgcagtttatgtgtttcatttgattgcttttctcacaataataaggtcattgatt--gtagTTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAG

upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 7
gtatattgttgat-attggctctctttctctctcatacctgaatatttc---agatg-actgacattttgttattg-----tgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG
 | | ||||   | | ||         || | |   | ||  || | ||   ||| | ||||   || | |   ||     | |  |  | ||      |||||| ||||| || ||  |||||||| |||| ||||||||||| || || |||||||| || || ||||||||||| ||||| || ||||||||||||
-tgtgttgtccttgactgatcgatagcctttatttgatctctatttctcttaagacgtactggttttctttagctgacagatataatattcttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG

upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 7
-----------------gtatattgttgatattggctctctttctctctcatacctgaata-tttcagatgactgacattttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG
                  |  ||| |   |||| ||||||| | | ||| |      |||| |||    |  ||||||      |||  | |  ||| |      | |||||||||||| || ||  |||||||| |||| |||||||| || || || |||||||| || ||  |||| ||||| ||||| || ||||||||||||
tttattggccttaactgatcgattatctttatttgctctctatttatcttaagatgcaatagttttctttacctgaca----aatataatattcttgat-----gacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG

upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 7
gtatattgttgatattggctctctttctctctcatacctgaatatttcagatgactgacattttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG
||||  | ||  |  | | |   | | |  ||  |   |   ||| | | |||    || || | || |  |     |  | |||  | ||||||||||||||| |||||||| ||| |||| |||||||| ||||| || ||||| || || | | | || |||||||||||||||||||| || |||
gtattattttctttcttgatgcttctattccttgtttgttgctatataatatgctgaactttcttttttatttaaactcctattttgacagTTGAAAAGGCCAAATATTTCTATATTGCTGGTTTTTTCCTGACTGTGTCCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAG

upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 7
gtatattgttgatattggctctctttctctctcatacctgaatatttcagatgactgacattttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG
||||  | ||  |  | | |   | | |  ||  |   |   ||| | | |||    || || | || |  |     |  | |||  | ||||||||||||||| |||||||| ||| |||| |||||||| ||||| || ||||| || || | | | || |||||||||||||||||||| || |||
gtattattttctttcttgatgcttctattccttgtttgttgctatataacatgttgaactttcttttttatttaaactcctattttgacagTTGAAAAGGCCAAATATTTCTATATTGCTGGTTTTTTCCTGACTGTGTCCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAG

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|209708530|gb|BW668141.1|BW668141
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCNTTTTNCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|10845490|gb|BF071116.1|BF071116
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|17518725|gb|BM187767.1|BM187767
EST:     CCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: CCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|192324906|gb|FK016092.1|FK016092
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|213598835|gb|DB968306.1|DB968306
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|209711575|gb|BW676820.1|BW676820
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|5688475|gb|AI941490.1|AI941490
EST:     GAAAATTGGGCATCCC                         CTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: GAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|193667347|gb|FK609753.1|FK609753
EST:     GAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|9440259|gb|BE440768.1|BE440768
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|151405346|gb|EV275160.1|EV275160
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACCGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|207703119|gb|GD684897.1|GD684897
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAGGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|151404672|gb|EV274486.1|EV274486
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|11687342|gb|BF594982.1|BF594982
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATNGGGCATTAG                         TTGAAAAG-CCAACTATTTCTACATTTCTGGCTTTCTCCTTACTGTATCTG
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|213611486|gb|DB959196.1|DB959196
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|9987590|gb|BE661698.1|BE661698
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGNATTTCTACATTTCTGGCTTTTTCCTCACTG
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTG
EST: gi|213597865|gb|DB958246.1|DB958246
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTG
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTG
EST: gi|151405163|gb|EV274977.1|EV274977
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|19937792|gb|BQ081423.1|BQ081423
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGNGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTATTTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTC
EST: gi|12773014|gb|BG237941.1|BG237941
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAGGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTG
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|21602656|gb|BQ612987.1|BQ612987
EST:     ATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: ATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|14126129|gb|BG790567.1|BG790567
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAG
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAG
EST: gi|15287897|gb|BI471788.1|BI471788
EST:     GAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: GAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|308098710|gb|HO760451.1|HO760451
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|15199748|gb|BI423990.1|BI423990
EST:     AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtatattgtt ... ttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgaatatttcagatgactgacattttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG
                gactgac  putative branch site (score: 2)
                                       tttgttttttc  putative PPT
                                       tttgttttttcaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattgttgatattggctctctttctctctcatacctgaatatttcagatgactgacattttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC