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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgccattattatggaaataaaagagacagttttgaatgggtattggattgatcaatttttgaaatttgtaactttgtgattgtctgttcgtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGG

Basic information

species Glycine max
transcript GLYMA18G48280.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 2
-atgccattattatggaaata--aaagagacagttttgaatg-ggtattggattgatcaatttttgaaatttgtaactttgtgattgtctgttcgtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGG
 | |      | || | | ||  ||| || |  | || ||   |||   || |  ||  | | ||||    |  ||  ||     | | ||| |      |||| ||||||||||| |||||||| |||||||||||||| || ||||| ||||| ||| 
taggtagaagtcattgcagtatgaaaaaggctttgttaaacatggttggggctctatataatattga---ctagaatcttcctcctttatgtgcacatcacagAGTACAGAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAG-
















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|192314147|gb|FK011519.1|FK011519
EST:     GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGA                         ATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
genomic: GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGGtgagtatcgt ... gtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
EST: gi|209723884|gb|BW675230.1|BW675230
EST:     GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGA                         ATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
genomic: GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGGtgagtatcgt ... gtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
EST: gi|15204687|gb|BI427455.1|BI427455
EST:     GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGA                         ATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
genomic: GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGGtgagtatcgt ... gtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
EST: gi|298165189|gb|HO011238.1|HO011238
EST:     GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGA                         ATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
genomic: GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGGtgagtatcgt ... gtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
EST: gi|213617560|gb|DB969272.1|DB969272
EST:     GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGA                         ATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
genomic: GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGGtgagtatcgt ... gtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
EST: gi|21676103|gb|BQ628454.1|BQ628454
EST:     GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGA                         ATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
genomic: GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGGtgagtatcgt ... gtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
EST: gi|213617292|gb|DB965191.1|DB965191
EST:     GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGA                         ATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
genomic: GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGGtgagtatcgt ... gtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
EST: gi|16995684|gb|BM085056.1|BM085056
EST:     GGGAACCTTGGAGATTGGAATGGA                         ATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
genomic: GGGAACCTTGGAGATTGGAATGGGtgagtatcgt ... gtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
EST: gi|21889121|gb|BQ742334.1|BQ742334
EST:     GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGA                         ATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
genomic: GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGGtgagtatcgt ... gtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
EST: gi|15815102|gb|BI787377.1|BI787377
EST:     GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGA                         ATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
genomic: GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGGtgagtatcgt ... gtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
EST: gi|21994280|gb|BQ785808.1|BQ785808
EST:     GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGA                         ATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT
genomic: GCTCAAAACATTCCCGATGCGGAGGAGGGAACCTTGGAGATTGGAATGGGtgagtatcgt ... gtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattgatcaatttttgaaatttgtaactttgtgattgtctgttcgtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGG
                     ttgtaac  putative branch site (score: 2)
         aatttttgaaatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgccattattatggaaataaaagagacagttttgaatgggtattggattgatcaatttttgaaatttgtaactttgtgattgtctgttcgtgctgcagaATACAGAACTGTTTCTGGAGTTGCTGGGCCATTGGTCATTCTTGATAAAGTTAAGG

-tgccatt
- - - - - - - -aaataaa
- - - - - - - - - - - - - - - - -tgaatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttgtg