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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaattgttgtggatgtgaaatcttttttaagtagccattcatgtcaaatgcccactcctttttatgtagccattcatgtcaaatgcttactcctttcagGATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATATATCCACTCTGGTGATGCTGATGCCCGTGCCAGAGATGCAACGGCTCCCC

Basic information

species Glycine max
transcript GLYMA16G18930.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G18930.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G26120.1 (Arabidopsis thaliana), 3'ss of exon 10
aaaattgttgtgga-tgtgaaatcttttttaagtagccat-tcatgtcaaatgcccactcc--tttttatgtagccattcatgtcaaatgcttactcctttcagGATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATATATCCACTCTGGTGATGCTGATGCCCGTGCCAGAGATGCA-ACGGCTCCCC
         ||  | ||     ||||||| | |||   || || ||||  |     ||     |||| || |||  | |         || |||    | | ||||||| ||||||||||| | |||||| |||||||||||| ||||| ||    | |     |  |||   || ||   ||  | |   | | |  |    | 
---------gtaaaatggccggtctttttgaggtatgaatgtcttgtcggacaagaacctgaattttgatctagaaact---------tggttatctatgttagGATCCAATGAGAGGTGGAATAGATGAGATGTTTGAAGATATAGTAACAGTGGTTCTGGGAGACGATCAAGAAGCGATTGGTAAAAGCGTAGATAGAAGGC-

upper sequence: GLYMA16G18930.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0011g02530.t01 (Vitis vinifera), 3'ss of exon 10
aaaattgttgtggatgtgaaatcttttttaagtagccattcatgtcaaatgcccactcctttttatgtagccattcatgtcaaatgcttactccttt--------cagGATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATATATCCACTCTGGTGATGCTGATGCCCGTGCCAGAGATGCAACGGCTCCCC
         |  ||||     |||||   | | |       || | ||||    |    ||       | |   || |    | |  |   ||||||        |||||||| ||||| ||||| | |||||||||||||||||||||||| ||    || ||  |   |||| | || ||||  || | |||||||  ||| || |
-------cagaagatg-attctctttcccatggaaatgagaatattaaatatgaaggaattaacgcaaaactgctcctactgacttgtagttccttttaaatttgcagGATCCAATGAGGGGTGGTAGAGATGATATGTTTGAAGATTTAGTTGCCATGATTCATGCAAATGATCCAGAAGCCCTAGCAAAAGATGCAGTGGCACCTC
















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|18734511|gb|BM528225.1|BM528225
EST:     CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAG                         GATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT
genomic: CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAGgtattgacca ... ctcctttcagGATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT
EST: gi|58017542|gb|CX704284.1|CX704284
EST:     CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAG                         GATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT
genomic: CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAGgtattgacca ... ctcctttcagGATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT
EST: gi|58024691|gb|CX711432.1|CX711432
EST:     CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAG                         GATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT
genomic: CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAGgtattgacca ... ctcctttcagGATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT
EST: gi|58018701|gb|CX705443.1|CX705443
EST:     CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAG                         GATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT
genomic: CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAGgtattgacca ... ctcctttcagGATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT
EST: gi|8286456|gb|BE024024.1|BE024024
EST:     CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAG                         GATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT
genomic: CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAGgtattgacca ... ctcctttcagGATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT
EST: gi|13791746|gb|BG654337.1|BG654337
EST:     CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAG                         GATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT
genomic: CTGAATCAATTTTGTACGAAGGGAAGACACATACAGATGTGTTTCTACAGgtattgacca ... ctcctttcagGATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatgcccactcctttttatgtagccattcatgtcaaatgcttactcctttcagGATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATATATCCACTCTGGTGATGCTGATGCCCGTGCCAGAGATGCAACGGCTCCCC
                                       tgcttac  putative branch site (score: 2)
                                       tgcttactcctttc  CT-rich tract
              tttttatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaattgttgtggatgtgaaatcttttttaagtagccattcatgtcaaatgcccactcctttttatgtagccattcatgtcaaatgcttactcctttcagGATCCTATGAGAGGTGGCAAAGATGATATGTTTGAAGATTTAGTAGCATATATCCACTCTGGTGATGCTGATGCCCGTGCCAGAGATGCAACGGCTCCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - gttgtgg
- - - - - - - - - - - - - - - - - - - -tcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgctt