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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctggtgtagtggtatccaagatcaaatgtttatgtaaccaaatcttcttaaaactggttatcatctgtaactaaaattttcattattgtcatggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG

Basic information

species Glycine max
transcript GLYMA05G27240.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 15
-cctggtgtagtggtatccaagatcaaatgttt----atgtaaccaaatcttctta-----aaactggttatcatctgtaactaaa-attttcattattgtcatggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG
   ||   |     | |  |       |  |||    |||    |  ||  |||||     || |||  |   ||   ||  |    ||| ||  |    ||||||  ||| ||||||||||||||||  ||||||||||||| || ||||| ||||||||||| ||  | |||||||||||||| || |||
gtttgacttttcatttttgacatgtgtacatttgcaaatgctgtcccattctcttaggtaaaagctgagttgaataaatatttttgcattatctgtggattcatgg--cagGTTGATGCTGCTATTGTCCGGATAATGAAGACGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAG
















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|16344341|gb|BI969936.1|BI969936
EST:     AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAG                         ATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAGgttaatgttc ... catggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
EST: gi|23733442|gb|BU764920.1|BU764920
EST:     AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAG                         ATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAGgttaatgttc ... catggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
EST: gi|12773136|gb|BG238063.1|BG238063
EST:     AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAG                         ATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAGgttaatgttc ... catggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
EST: gi|31471408|gb|CD413436.1|CD413436
EST:     AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAG                         ATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAGgttaatgttc ... catggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
EST: gi|19346215|gb|BM891095.1|BM891095
EST:     AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAG                         ATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGT
genomic: AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAGgttaatgttc ... catggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGT
EST: gi|27809423|gb|CB063845.1|CB063845
EST:     AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAG                         ATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAGgttaatgttc ... catggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
EST: gi|209698239|gb|BW667542.1|BW667542
EST:     CCATGACCGTCAATATCAG                         ATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
genomic: CCATGACCGTCAATATCAGgttaatgttc ... catggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
EST: gi|7690871|gb|AW759008.1|AW759008
EST:     AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAG                         ATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAGgttaatgttc ... catggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
EST: gi|31305219|gb|CD390422.1|CD390422
EST:     AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAG                         ATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAGgttaatgttc ... catggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC
EST: gi|7686211|gb|AW756922.1|AW756922
EST:     AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAG                         ATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTACTCAC
genomic: AGGAGAACACAAGCACCACCGAAAGAGTTTTCCATGACCGTCAATATCAGgttaatgttc ... catggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttaaaactggttatcatctgtaactaaaattttcattattgtcatggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG
                        aactaaa  putative branch site (score: 2)
                     tgtaactaaaattttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctggtgtagtggtatccaagatcaaatgtttatgtaaccaaatcttcttaaaactggttatcatctgtaactaaaattttcattattgtcatggttcagATTGATGCTGCTATTGTGAGGATAATGAAGACTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG

- - - gtagtgg
- - - - - - - - - - - - - - - - - - aaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -actggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catctgt