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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttgtttttattttgctggttcttgttatgtgttaagctattgttggagaatgaatagattgattcatggtttgtgatttctttgaataatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT

Basic information

species Glycine max
transcript GLYMA04G33880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G33880.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
tgtttgtttttattttgctggttcttgttatgtgttaagct--attgttggagaatgaatagattgattcatggtttgtgatttctttgaataatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT
   |   | |||||||| ||    |   ||| |    |  |  |||||| ||  ||   |    | ||  ||  | | |  || ||||    | | || |||||||||||| || || ||||| || |  || |||||||||||||| ||||||||||||||||| ||||| || ||||| || |||||  | ||||| |||
--gtaagtattattttgttgtaattcaatattttgccattttgattgtttgattatttctgttattatatata-tatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT

upper sequence: GLYMA04G33880.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G130548_T01 (Zea mays), 3'ss of exon 2
tgtttgtttttattttgctggttcttgttatgtgttaagctattgttggagaatgaata--gattgat--tcatggtttgtgatttctttgaataatgctt-----cagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT
         | | ||  |    |    || |   | ||  ||| |      | || ||   | |||||  | || | || || |||   | | |     ||     ||| |||||||| ||||| |||||||| |  || ||| |||| ||||| |||||||||||||| || ||||| || ||||| || ||||| || || || || 
--------gtaagttaacccactaaccttttagataaacatatagacactaactgtattccgtttgatggttattgcttctgttttacctcattggccattttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCAATGGCTCACGTACTGGGTGCTGTACTCATTTATCACTCTATTCGAGCTC

upper sequence: GLYMA04G33880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
--tgtttgtttt-tattttgctggttcttgttatgtgttaagctattgttggagaatgaatagattgattcatggtttgtgatttctttgaataatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT
  ||| |||| | || | ||  | ||     | ||||||    | || |  |||||  ||| | ||||  | |   || || |    | |  |  |    ||||||||||||  ||||||||||||||| |||||| ||||||||||| |||||||||||||| || |||||| | || ||  ||||||| ||||| || || 
catgtatgttctataatatgtggtttgaatgtttgtgttttagttttctgagagaa--aattgcttgaaacttttgttttggtgggct-ggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC

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|298182365|gb|HO026540.1|HO026540
EST:     GCCTTTGCTTAGTCTTGCCTATCCTCT                         ATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCA
genomic: GCCTTTGCTTAGTCTTGCCTATCCTCTgtaagtgcac ... aatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCA
EST: gi|298190156|gb|HO032277.1|HO032277
EST:     GCCTTTGCTTAGTCTTGCCTATCCTCT                         ATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCA
genomic: GCCTTTGCTTAGTCTTGCCTATCCTCTgtaagtgcac ... aatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCA
EST: gi|208224477|gb|GE021844.1|GE021844
EST:     GCCTTTGCTTAGTCTTGCCTATCCTCT                         ATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCA
genomic: GCCTTTGCTTAGTCTTGCCTATCCTCTgtaagtgcac ... aatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCA
EST: gi|207836568|gb|GD806565.1|GD806565
EST:     GCCTTTGCTTAGTCTTGCCTATCCTCT                         ATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGA
genomic: GCCTTTGCTTAGTCTTGCCTATCCTCTgtaagtgcac ... aatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGA
EST: gi|298176531|gb|HO023118.1|HO023118
EST:     GCCTTTGCTTAGTCTTGCCTATCCTCT                         ATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGGCCAGCA
genomic: GCCTTTGCTTAGTCTTGCCTATCCTCTgtaagtgcac ... aatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCA
EST: gi|298181555|gb|HO025730.1|HO025730
EST:     GCCTTTGCTTAGTCTTGCCCATCCTCT                         ATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCA
genomic: GCCTTTGCTTAGTCTTGCCTATCCTCTgtaagtgcac ... aatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggagaatgaatagattgattcatggtttgtgatttctttgaataatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT
              gattgat  putative branch site (score: 4)
                                 atttctttgaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttgtttttattttgctggttcttgttatgtgttaagctattgttggagaatgaatagattgattcatggtttgtgatttctttgaataatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT

tgtttgt
- - - - - - - -tgctggt
- - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - gctattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttgtg