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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttcttttatgatgaaagaaataaatggcaatgcggatgggacatttgatgtaggaaattttttatgatgcttataactatctctggaatgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAGAAGAGGGATGCTATTGACACAAAGAACCAGGCAGACTCTGTGGTATACC

Basic information

species Glycine max
transcript GLYMA12G28750.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G28750.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g14070.1 (Oryza sativa), 3'ss of exon 7
gcttcttttatgatgaaagaaataaatggcaatgcg-gatgggacatttga-tgtag-gaaattttttatgatgcttataactatctctggaatgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAGAAGAGGGATGCTATTGACACAAAGAACCAGGCAGACTCTGTGGTATACC
  ||| | || |   | |  | ||     |  |  | || |  |||  ||  |  |  |||   |   ||      |  ||| |  | | |  |    |  |||| |||||||||||  | || ||||| || ||| |  |||| ||||||||||| || ||||| ||||| || || |||||||||||||||||||| ||||
agttcctctagggaaacaacactatgctcctgtaagcgaagatacaaatgcctacattgaagcataacattcaatctgaaacaacattttgtgtt---tgtagGTTGAGAGAATGGTGGAAGAGGCTGACAAGTTTGCTCAGGAGGACAAAGAGAAAAGAGATGCCATTGATACCAAAAACCAGGCAGACTCTGTGGTCTACC

upper sequence: GLYMA12G28750.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G001500_T01 (Zea mays), 3'ss of exon 6
-gcttcttttatgatgaa--agaaataaatggcaatgcggat---gggacatttgatgtaggaaattttttatgatgcttataactatctctggaatgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAGAAGAGGGATGCTATTGACACAAAGAACCAGGCAGACTCTGTGGTATACC
   | ||   ||  || |  |||     |||    |||  ||      |||  |  |      | |  |  ||||    |  ||||| |||          | ||||| |||||||||||| | ||||| || || ||| | ||||| |||||||||||||| ||||| || ||||| || |||||||| ||||| ||||| ||||
atttcctaccattctgtagtagagtagtatgattctgctaattccataacaaatagtacctacattggtgcatgaacgcttcaactacctccttt------tgcagGTTGAGAGAATGGTAGAAGAAGCCGATAAGTTTGCCAAGGAGGACAAAGAGAAGAGAGATGCAATCGACACCAAAAACCAGGCGGACTCAGTGGTCTACC

upper sequence: GLYMA12G28750.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g03310.t01 (Vitis vinifera), 3'ss of exon 7
-----gcttcttttatgatgaaagaaataaatgg-caatgcggatgggacatttgatgtaggaaattttttatgatgcttataactatctctggaatgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAGAAGAGGGATGCTATTGACACAAAGAACCAGGCAGACTCTGTGGTATACC
     | |||||      |  |   | |   |   |||     |     ||  |    | ||| |  | | |          || | | |   |    | || ||||||||||| ||||| | |||||| ||||  ||| | ||||| ||||| |||||||| ||||| || || |||||||| || || || |||||||| ||||
ttagggtttcttggggagtcgacatagttcttactcaacttctaatttgcacctataatgggacagctctgacag------aaaatgtgttgtgggaaatatgcagGTGGAGAGGATGGTTAGCGAAGCAGAGAGGTTTGCAAAGGAGGACAAGGAGAAGAGAGATGCCATAGATACAAAGAATCAAGCTGATTCTGTGGTCTACC

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|209697077|gb|BW667069.1|BW667069
EST:     ACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAG                         GTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
genomic: ACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAGgtatccacta ... tgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
EST: gi|213596145|gb|DB977507.1|DB977507
EST:     TAGCACCTTGCCTTCAGATGAG                         GTTTAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
genomic: TAGCACCTTGCCTTCAGATGAGgtatccacta ... tgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
EST: gi|16996030|gb|BM085402.1|BM085402
EST:     AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAG                         GTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
genomic: AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAGgtatccacta ... tgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
EST: gi|298192331|gb|HO036413.1|HO036413
EST:     AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAG                         GTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
genomic: AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAGgtatccacta ... tgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
EST: gi|192309717|gb|FK001023.1|FK001023
EST:     AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAG                         GTGGAGAGAATGGTAAACGAAGCTGGGAAATTTTCGAAGGAAGACAAAGAG
genomic: AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAGgtatccacta ... tgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
EST: gi|192320004|gb|FK013010.1|FK013010
EST:     AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAG                         GTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
genomic: AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAGgtatccacta ... tgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
EST: gi|22522446|gb|BU081257.1|BU081257
EST:     AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAG                         GTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
genomic: AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAGgtatccacta ... tgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
EST: gi|209712555|gb|BW653711.1|BW653711
EST:     AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAG                         GTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
genomic: AGAAACAAGATATTACCATCACTGGTGCTAGCACCTTGCCTTCAGATGAGgtatccacta ... tgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
EST: gi|151402150|gb|EV271963.1|EV271963
EST:     GAAACAAGATATTACCATCACTGGTGCTAGCACCTTCGCCTTCAGATGAG                         GTGGAGAGAATGGTAAACGAAGCT
genomic: GAAACAAGATATTACCATCACTGGTGCTAGCACCTT-GCCTTCAGATGAGgtatccacta ... tgaaatacagGTGGAGAGAATGGTAAACGAAGCT
EST: gi|192320003|gb|FK013009.1|FK013009
EST:     GTGCTAGCACCTTGCCTTCAGATGAG                         GTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG
genomic: GTGCTAGCACCTTGCCTTCAGATGAGgtatccacta ... tgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatgtaggaaattttttatgatgcttataactatctctggaatgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAGAAGAGGGATGCTATTGACACAAAGAACCAGGCAGACTCTGTGGTATACC
                           ttataac  putative branch site (score: 2)
           aaattttttatgatgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttcttttatgatgaaagaaataaatggcaatgcggatgggacatttgatgtaggaaattttttatgatgcttataactatctctggaatgaaatacagGTGGAGAGAATGGTAAACGAAGCTGAGAAATTTTCGAAGGAAGACAAAGAGAAGAGGGATGCTATTGACACAAAGAACCAGGCAGACTCTGTGGTATACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
gcttctt
- - - - - - - - - -aaataaa
- - - - - - - - - - - - - - gcaatgc
- - - - - - - - - - - - - - - - - -ggatggg
- - - - - - - - - - - - - - - - - - - - - - - -tgatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctgga