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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatgacaccttagctttttcatggaatatgtgcatatttatgctagttctgctctgcctttttatttgactttttaatctggaattttgtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTCTCGAATTTTGGAATA

Basic information

species Glycine max
transcript GLYMA10G36650.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G36650.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g40710.1 (Oryza sativa), 3'ss of exon 1
-tttatgacaccttagctttttcatggaatatgtgcatatttatgctagttctgctctgcctttttatttgactttttaatctgga-attttgtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTCTCGAATTTTGGAATA
  | |   ||   |  | |   | | |  |  |||  |  ||      | |  | | ||| | |||| |  | |  | | ||||   ||     |    ||||||||| |||||||| ||||| || ||  ||||||||||||| ||||| || || ||||||||| | ||||| |||||||||||||| |||||||| || 
aataaaagcagggtgacctagacttaggttcggtgttttgttgaatagggtaagatttgcttgtttact--aatggtgattctgatcatcaaaatctcgcagATGGGCTATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTACGCAACCGGCTCGGATTTTGTTCAACAAGTGAAGATCCTTCTCTCCAATTTTGGGATT

upper sequence: GLYMA10G36650.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G019807_T01 (Zea mays), 3'ss of exon 1
-----tttatgacaccttagctttttcatggaatatgtgcatatttatgctagttctgctctgcctttttatttgactttttaatctggaattttgtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTCTCGAATTTTGGAATA
     |  | || |  |   | |    ||  |  | ||   |   || | ||   | ||| || || | |      ||  || | || |       | |   ||| ||||| |||||||| ||||| || ||  ||||||||||||||||||| || || ||||||||| | ||| | |||||||||||||| ||||||||||| 
aaaaatgcaagataggtagacgtaaggattcaccacgttgttgagtacgttaagacagct-tgtctctatgc---gctaattcaccttgctacacatcttg-cagGTGGGCCATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTATGCAACAGGCTCGGATTTTGTTCAGCAAATGAAGATCCTTCTCTCCAATTTTGGAATT

upper sequence: GLYMA10G36650.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G143469_T01 (Zea mays), 3'ss of exon 1
--tttatgacaccttagctttttcatggaatatgtgcatatttatgctagttctgctctgcctttttatttgactttttaatctggaattttgtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTCTCGAATTTTGGAATA
  |  | ||    |          ||  |  | || | |   || | ||     ||||  |  | |    | | |  | |   |   |      ||   ||| ||||| |||||||| ||||| || ||  ||||||||||||| ||||| || || ||||||||| | ||| | ||||||||||| || ||||| ||||| 
aatacacgatgggtagatgcaaagattcaccacgttcttgagtaggttaaggaagctcatctctatgcgctaattcatcagctttctacaaacctt--gcagGTGGGCCATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTACGCAACAGGCTCTGATTTTGTTCAGCAATTGAAGATCCTTCTTTCCAATTTCGGAATT

upper sequence: GLYMA10G36650.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G34000.1 (Arabidopsis thaliana), 3'ss of exon 1
-tttatgacaccttagcttttt-catggaatatgtgcatatttatgctagttctgctctgcctttttatttgactttttaatctg-gaattttgtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTCTCGAATTTTGGAATA
 || |||   | | |  ||    |||  |     |  |  || |  || || | | |    ||   ||    |    | | |||| |  ||||||||    || ||||| ||||||||||| || |||||  |||| |||||||||||||| ||||||||  ||||||||||||| |||||||||||||| ||||| || || 
attgatgtttcttcaaattcagacatatatagcctaaagtttcacacttgt-cagttggtactgcctagacaagagataactctgtgtgttttgttt--gtagGTGGGCTATGTTTGGTTTCGCAGTTGGTATGCTCACAGAGTATGCAACAGGATCAGACCTTGTTGATCAAGTTAAGATCCTTCTCTCAAATTTCGGCATT

upper sequence: GLYMA10G36650.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
---tttatgacaccttagctttttcatggaatatgtgcatatttatgctagttctgctctgcctttttatttgacttt---ttaatctggaattttgtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTCTCGAATTTTGGAATA
   ||||| | || |||   | ||     | |||     ||||| | |     |   |||  ||| ||| |||  | |   |   ||||| || ||  |    ||||||||||||||| ||||||||||||||  ||||||||||||| ||||| || || || ||||||||||||||||||||||||||||| |||||||| |||
tcctttataa-acattattatgttggccta-tattaatgtatttcttcatcagccaatctagcttcttacttgggtctgtctctgtctgggatgttaat----cagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA

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|20498129|gb|BQ273059.1|BQ273059
EST:     CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAG                         ATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
genomic: CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAGgtaaaaaaac ... gtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
EST: gi|192309179|gb|FG999098.1|FG999098
EST:     CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAG                         ATGGGCAATGTTTGGTTTTGCTGTTGGATTGTTAACAGAGTATGCAACGGG
genomic: CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAGgtaaaaaaac ... gtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
EST: gi|151403235|gb|EV273045.1|EV273045
EST:     CAGGGTCCTTTCTTTGGATTCAT-GGCAAAAATGAGATTAGCAATGGAAG                         ATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
genomic: CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAGgtaaaaaaac ... gtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
EST: gi|151399144|gb|EV269015.1|EV269015
EST:     CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAG                         ATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
genomic: CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAGgtaaaaaaac ... gtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
EST: gi|31455996|gb|CD398024.1|CD398024
EST:     CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAG                         ATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATCCAACGGG
genomic: CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAGgtaaaaaaac ... gtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
EST: gi|31475038|gb|CD417066.1|CD417066
EST:     CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAG                         ATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
genomic: CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAGgtaaaaaaac ... gtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
EST: gi|31455907|gb|CD397935.1|CD397935
EST:     CAGGGTCCTTTCTTTGGAGTCATTGGCAAAAATGAGATTAGCTATGGAAG                         ATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
genomic: CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAGgtaaaaaaac ... gtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
EST: gi|192309178|gb|FG999097.1|FG999097
EST:     CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAG                         ATGGGCAATGTTTGGTTTTGCTGTTGGATTGTTAACAGAGTATGCAACGGG
genomic: CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAGgtaaaaaaac ... gtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
EST: gi|31456706|gb|CD398734.1|CD398734
EST:     CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAG                         ATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
genomic: CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAGgtaaaaaaac ... gtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
EST: gi|31311500|gb|CD396703.1|CD396703
EST:     CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAG                         ATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG
genomic: CAGGGTCCTTTCTTTGGATTCATTGGCAAAAATGAGATTAGCAATGGAAGgtaaaaaaac ... gtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttctgctctgcctttttatttgactttttaatctggaattttgtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTCTCGAATTTTGGAATA
                            ttttaat  putative branch site (score: 3)
                                         ttttgtttc  putative PPT
               tttttatttgactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatgacaccttagctttttcatggaatatgtgcatatttatgctagttctgctctgcctttttatttgactttttaatctggaattttgtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTCTCGAATTTTGGAATA

- - - acacctt
- - - - - - - - - - -catggaa
- - - - - - - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - - - - - - tatgcta