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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctcttgataggtagttggaattattgattcttaaaaatatgctagaacttgctgaagactgaaatggctttgtgttcttttggacaactgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGACCAGTTCTCGCCTGAATGTCTCCTTGATTGCCTGGATCTTTCAACAGAGC

Basic information

species Glycine max
transcript GLYMA12G02620.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G158679_T01 (Zea mays), 3'ss of exon 3
----atctcttgataggtagttggaattattgattcttaaaaatatgctagaacttgctgaagactgaaatggctttgtgttcttttggacaactgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGACCAGTTCTCGCCTGAATGTCTCCTTGATTGCCTGGATCTTTCAACAGAGC
    | | | | ||   |  ||||  | ||  |  || | ||    | | |   || | | |   ||| | | ||  || |  | |   |    |    ||||||| || ||  ||||  | || || ||||| |||||||||||||| || || |||||||| || ||||||||||| |||||| ||||||| ||| | ||||
aaacagcacat-atttttctttggtctaatatagcctaataatggaggtgggtatttccgta--ttgatacg-ctcagtctaatatcttattttttttctgcagAACGGTAAATCTTGCTTGGGTGAGATAATTTATCGATACATAACAGCTGAGCAGTTCTCACCAGAATGTCTCCTAGATTGCTTGGATCTATCATCCGAGC

upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G105253_T01 (Zea mays), 3'ss of exon 3
--atctcttgat---aggtag-ttggaattattgattcttaaaaatatgctagaacttgc-tgaagactgaaatggctttgtgttcttttggacaactgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGACCAGTTCTCGCCTGAATGTCTCCTTGATTGCCTGGATCTTTCAACAGAGC
   |   ||| |   |  ||| |||     | | || |   |    |||     | ||   |   || |||    |  |  | |  | |       ||    |||||| ||| ||  ||||  | || || ||||| || ||||||||||| || || |||||||| || |||||||| || |||||| ||||||| ||| | || |
gttttctttggtccaacatagcttgtctccagtaatacaggagtggatgtggatatttttgtagtgattgacccagtctaatatcttat-------ctttcttgcagAGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAGCAGTTCTCACCAGAATGTCTACTGGATTGCTTGGATCTATCATCGGAAC

upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g03620.t01 (Vitis vinifera), 3'ss of exon 4
atctcttgataggtagttggaattattgattcttaaaaatatgctagaacttgctgaagactgaaatggctttgt-gttctt--ttggacaactgaaat-gcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGACCAGTTCTCGCCTGAATGTCTCCTTGATTGCCTGGATCTTTCAACAGAGC
   | ||||     | ||  ||| ||  |   |  |    ||||      ||  | ||        |   || || | | ||  |||  ||| ||  ||  |||||||| || || ||||| || ||||| |||||||| ||||| || || || |||||||| || ||||||||||||||||||||||| || ||| |||| |
---ttttgaacaaca-ttataatcatgaagagtatatggaatgcatcttgtttttcaatttcagttttatttggtagctattcattgctcaattgccattacagAATGGGAAAGCATGTCTGGGTGATATCATCTATCGCTACATCACTGCTGAACAGTTCTCCCCAGAATGTCTCCTTGATTGCCTGGACCTATCATCAGAAC

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|193473169|gb|FK436716.1|FK436716
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|193566071|gb|FK525932.1|FK525932
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|208321386|gb|GE125515.1|GE125515
EST:     TTCTTGCTGAAATGGAAATTCCGGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGC
EST: gi|193630434|gb|FK579969.1|FK579969
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|193527737|gb|FK485927.1|FK485927
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGG
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGG
EST: gi|207709011|gb|GD690511.1|GD690511
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|193617070|gb|FK570662.1|FK570662
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|193669777|gb|FK613679.1|FK613679
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|208106047|gb|GD904260.1|GD904260
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTG
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTG
EST: gi|193570447|gb|FK526274.1|FK526274
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|193675979|gb|FK617375.1|FK617375
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|193728264|gb|FK665034.1|FK665034
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAG-CCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|193393054|gb|FK357926.1|FK357926
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGG
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGG
EST: gi|207803379|gb|GD775796.1|GD775796
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGG
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGG
EST: gi|208319600|gb|GE114531.1|GE114531
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGG
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGG
EST: gi|207720592|gb|GD703525.1|GD703525
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|207755216|gb|GD729811.1|GD729811
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTC
EST: gi|193672262|gb|FK617148.1|FK617148
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|193560179|gb|FK517582.1|FK517582
EST:     CTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: CTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|193638199|gb|FK586693.1|FK586693
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGAC
EST: gi|207819586|gb|GD790822.1|GD790822
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGG
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGG
EST: gi|208334150|gb|GE127895.1|GE127895
EST:     TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAG                         AATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACG
genomic: TTCTTGCTGAAATGGAAATTCCCGGTGCCTACATTGAGTCCTTGCCCAAGgtaagtaatg ... tgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaacttgctgaagactgaaatggctttgtgttcttttggacaactgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGACCAGTTCTCGCCTGAATGTCTCCTTGATTGCCTGGATCTTTCAACAGAGC
                               ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctcttgataggtagttggaattattgattcttaaaaatatgctagaacttgctgaagactgaaatggctttgtgttcttttggacaactgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGACCAGTTCTCGCCTGAATGTCTCCTTGATTGCCTGGATCTTTCAACAGAGC

- - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gactgaa