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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttatattgccataatttgcatcgtcaaaatttgtctttctcaatgaccagtcccactggtttctcttgactcttgagttctgtttataaatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTATATGCAAATGGATGGAGAACCCTGGAAACAGCCATTGAGCAAGGACTTCT

Basic information

species Glycine max
transcript GLYMA13G01360.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G01360.2 (Glycine max), 3'ss of exon 11
lower sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 9
----ctttatattgcca--taatttgcatcgtcaaaatttgtctttctcaatgaccagtcccactggtt--tctcttgactcttgagttctgtttataaatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTATATGCAAATGGATGGAGAACCCTGGAAACAGCCATTGAGCAAGGACTTCT
      | | |||  ||  ||   | |||    |    |  | | | ||  || | | ||    | | |  | |    |  |||| ||| |    |  ||     |||||  |||| ||  |  ||||  | ||||| ||| | |||||| | || | |||||||||||||||||| || |||||||||||  ||| ||  |||| ||
catatctaacatttacaattacactacataaatatggatgatatatgtctttggcaaatcgtggtagctaatgtgcaaaaacttgggtttta---acgaa-----cagGCGGCAGCGATAAGGCTGGAGATAAGAGGAGGAGACTGGAAAGATGCGTTTATGCAAATGGATGGAGAGCCATGGAAACAGCCTATGACCAGAGACTACT

upper sequence: GLYMA13G01360.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 11
---ctttatattgccataatttgcatcgtcaaaatttgtctt---tctcaatgaccagtcccactggtttctcttgactcttgagttctgtttataaatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTATATGCAAATGGATGGAGAACCCTGGAAACAGCCATTGAGCAAGGACTTCT
    |   | || |||| ||  |  |  |  |   |  | ||   |    |   | |  |        |||  ||||    | |||| | |   ||  ||||||||||  |||| || ||||||||| ||||||||||| |||||||  | || |||||||| |||||||| || || |||||||||||| | | ||| || || |
gatttaagtgtttccatcata-gtgttattgatgctgatgttggattctgaaatctatgcttttataattccattgaa---taagttttatgggta--tctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATATATGCAGATGGATGGGGAGCCATGGAAACAGCCAATAAACAATGAGTTTT
















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|192332064|gb|FK026344.1|FK026344
EST:     ACGCATCGTTTGTCATGGTGGAACTGATCTCTGCTAAGCACTTAGCTCAG                         GCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTAT
genomic: ACGCATCGTTTGTCATGGTGGAACTGATCTCTGCTAAGCACTTAGCTCAGgtaccacagt ... aatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTAT
EST: gi|51337091|gb|CO980957.1|CO980957
EST:     ACGCATCGTTTGTCATGGTGGAACTGATCTCTGCTAAGCACTTAGCTCAG                         GCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTAT
genomic: ACGCATCGTTTGTCATGGTGGAACTGATCTCTGCTAAGCACTTAGCTCAGgtaccacagt ... aatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTAT
EST: gi|302141303|gb|HO212179.1|HO212179
EST:     ACGCATCGTTTGTCATGGTGGAACTGATCTCTGCTAAGCACTTAGCTCAG                         GCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTAT
genomic: ACGCATCGTTTGTCATGGTGGAACTGATCTCTGCTAAGCACTTAGCTCAGgtaccacagt ... aatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTAT
EST: gi|15203215|gb|BI425983.1|BI425983
EST:     ACGCATCGTTTGTCATGGTGGAACTGATCTCTGCTAAGCACTTAGCTCAG                         GCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTAT
genomic: ACGCATCGTTTGTCATGGTGGAACTGATCTCTGCTAAGCACTTAGCTCAGgtaccacagt ... aatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTAT
EST: gi|192332065|gb|FK026345.1|FK026345
EST:     ACGCATCGTTTGTCATGGTGGAACTGATTTTTGCTAAGCACTTAGCTCAG                         GCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTAT
genomic: ACGCATCGTTTGTCATGGTGGAACTGATCTCTGCTAAGCACTTAGCTCAGgtaccacagt ... aatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaccagtcccactggtttctcttgactcttgagttctgtttataaatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTATATGCAAATGGATGGAGAACCCTGGAAACAGCCATTGAGCAAGGACTTCT
                    tcttgac  putative branch site (score: 3)
                                               tctttc  putative PPT
                                     tgtttataaatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttatattgccataatttgcatcgtcaaaatttgtctttctcaatgaccagtcccactggtttctcttgactcttgagttctgtttataaatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTATATGCAAATGGATGGAGAACCCTGGAAACAGCCATTGAGCAAGGACTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG