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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtttcttttgctgctatcatgtttccaatagatcgataaagacacgcatatcctgttttctaactacacttgttatgcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCCTATTACCGCCGCTTGAGGTGGTCAGTTCTAAAGTCTCGCAAGCTGGTTC

Basic information

species Glycine max
transcript GLYMA16G06700.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 7
------gtctgttt-cttttgctgctatcatgtttccaata--gatcgataaagacacgcatatcctgttttctaactacacttgttatgcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCCTATTACCGCCGCTTGAGGTGGTCAGTTCTAAAGTCTCGCAAGCTGGTTC
        || ||  |||     |||   ||   || | |     || ||         ||||||||| |  | | | || |     || ||| || |||||||| | |||||||| ||| |||| ||| | || || || || |||||||| ||||||||| |||||||||||||  | ||||| || |||||||| |
gtaacaacctcttgacttaaatcgctcagattgctctattgctattcaatttgctactccatatcctgatcacaatccactcaaaa-atccat-tgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCCTACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGAAAGCTGGTCC

upper sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G032367_T04 (Zea mays), 3'ss of exon 6
-------gtctgtttcttttgctgctatcat--gtttccaatagatcgataaagacacgcatatcctgttttctaactacacttgttatgcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCCTATTACCGCCGCTTGAGGTGGTCAGTTCTAAAGTCTCGCAAGCTGGTTC
           |   |||   |   || |    |||| |  |    |  |  |       |||     | | || |  |||  |   ||      | |||||||| | |||||||| ||| |||| ||| | || || ||||| ||||| || ||||||||| |||||||||||||  | ||||| || |||||||| |
gtaacaacctcgcgacttaatcaattaactgcagtttgcgctgttgcttttcaatttgctataatacttatcctgatcacaactcaaatttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCATACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGTAAGCTGGTCC

upper sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 7
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 6
-gtc-tgtttcttttgctgctatc---atgtttccaatagatcgataaagacacgc---atatcctgttttctaactacacttgtt--atgcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCCTATTACCGCCGCTTGAGGTGGTCAGTTCTAAAGTCTCGCAAGCTGGTTC
 ||| ||||  || |    | | |   |     ||  || | ||| ||    || |    |     | | |||    ||  | |||  |||  | |||||||||| || |||||||||||  ||||||| ||||| || ||||| ||||| |||||| |  |  |||  |||||||| || || || || ||||| ||||
cgtcatgttggttctaaaccgacccaaaaaaacccgctataccgagaatccaactctttgtgcttagatatctgttaacgttggttgtatgtgtgtgcagATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCGTATTACAGGAGACTGAAATGGTCAGTACTCAAATCCCGTAAGCTTGTTC

upper sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 6
-----gtctgtttcttttgctgctatcatgtttccaatagatcgataaagac-acgcat--atcctgttttctaactacacttg---ttatgcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCCTATTACCGCCGCTTGAGGTGGTCAGTTCTAAAGTCTCGCAAGCTGGTTC
        ||    |   | ||  || || | |  || ||| |  |     | | | |   ||     |||||||| | | |||   ||    | |||||||||||||||||||||||||||||  ||||| | ||||| || || || || || ||||| ||| | |  |||||| |  | ||||| || |||||| || 
attagaaatgggaatcgagatgg-attatttgtgaaaaagagcatttttttccaagtaacaataactatttctaaccaaatttggcttttaaaaaatgcagATGGGATTTAAATGGATATTTGTGTTGTCACTTGCACTTCTCCAAGCAGCTTACTACCGACGCCTAAAATGGTCAATCTTCAAGTCCCGTAAGCTGATTG

upper sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 7
gtctgtttcttttgctgct--atcatgtttccaatagatcgataaagacacgcatatcctgttttctaactacacttgttatgcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCCTATTACCGCCGCTTGAGGTGGTCAGTTCTAAAGTCTCGCAAGCTGGTTC
      |  ||| ||| ||  ||    | |||| ||    ||  || |      ||   |||||  | |||  |  | |  |  | ||||||||||| || |||||||||||| |||| ||| ||||||||||||| ||||| |||| | | || ||||||||||| ||    |||||||| |||||| || 
-----gtaatttggcttctgaattccctgtccattatgatgagtaaaatt----tagtttgttta-tgactttagatctcttcaaaatgcagATGGGGTTCAAATGGATATTTTTACTTTCACTGGCACTACTTCAAGCTGCTTATTTCAGGCGATTGAGGTGGTCTGTCTACAAGTCTCGTAAGCTGATTG

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|254330992|gb|GR842257.1|GR842257
EST:     TGTCATTCTTAACTTGGGCCGCCGAACCCGAGATGGAAGAGAGAAAACTG                         ATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCC
genomic: TGTCATTCTTAACTTGGGCCGCCGAACCCGAGATGGAAGAGAGAAAACTGgtctgtttct ... gcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCC
EST: gi|214004891|gb|DB989037.1|DB989037
EST:     GTCATTCTTAACTTTTG-CGACCGAACCCGAGATGGAAGAGAGAAAACTG                         ATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCC
genomic: GTCATTCTTAACTTGGGCCG-CCGAACCCGAGATGGAAGAGAGAAAACTGgtctgtttct ... gcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCC
EST: gi|254314652|gb|GR829645.1|GR829645
EST:     TGTCATTCTTAACTTGGGCCGCCGAACCCGAGATGGAAGAGAGAAAACTG                         ATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCC
genomic: TGTCATTCTTAACTTGGGCCGCCGAACCCGAGATGGAAGAGAGAAAACTGgtctgtttct ... gcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCC
EST: gi|213601038|gb|DB983713.1|DB983713
EST:     TGTCATTCTTAACTTGGGCCGCCGAACCCGAGATGGAAGAGAGAAAACTG                         ATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCC
genomic: TGTCATTCTTAACTTGGGCCGCCGAACCCGAGATGGAAGAGAGAAAACTGgtctgtttct ... gcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgataaagacacgcatatcctgttttctaactacacttgttatgcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCCTATTACCGCCGCTTGAGGTGGTCAGTTCTAAAGTCTCGCAAGCTGGTTC
                          ttctaac  putative branch site (score: 1)
                        ttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtttcttttgctgctatcatgtttccaatagatcgataaagacacgcatatcctgttttctaactacacttgttatgcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCCTATTACCGCCGCTTGAGGTGGTCAGTTCTAAAGTCTCGCAAGCTGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG