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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgaaggaggtttaagcattgatccatccaacttgtgaattattgcttctgtacattacttttctgtttccactgtgtattcttacaacttccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG

Basic information

species Glycine max
transcript GLYMA09G24630.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G24630.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g38970.1 (Oryza sativa), 3'ss of exon 2
-------gtgaaggaggtttaagcattgatccatccaacttgtgaattattgcttctgtacattacttttctgtttccactgtgtattcttacaacttccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG
        | |   | | | ||| || | |  || |    |  || |||      | | | | ||  |||   |||  ||||  | || |   ||   |  || |||| ||||||||| | |||||||||||||||||||| ||| ||| ||| ||||  || |||||| |   |
tgtttgtcttatccatgct-aagtatggttgtattcctgctcagatttaaaatgacag-ataatatattt---ttttaactg-atcttgtgttaaaaactgtg-cagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG

upper sequence: GLYMA09G24630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G162292_T02 (Zea mays), 3'ss of exon 2
gtgaaggaggtttaagcattgatccatccaacttgtgaattat-tgcttctgtacattacttttctgtttccactg-tgtattcttacaacttccatgac-----agGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCA-TTACGG-------------------------------
       |  ||| | |  || | |   || |    |  |    || || |||   |||  |||    | |||      || ||||  |   |   | ||     ||||||||| ||| | ||||||||||| |||||||||||| |||  || ||||  || |||||| ||| ||                               
-------aatttttatctatgttgctagcaccagaggcctagcatgattgtgtttcttaggtttgaaatgccatgaacttactcttttattctgtctaaccttgcagGTTGGGTGAATCGCTTTGCCAATGCCGGTGATACTGCTGTGGTTGTTGCTGAGAACACAGCAGTTAAGGTAATTTCAGAATTTGTTGCTGTGATACAATG

upper sequence: GLYMA09G24630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G162292_T01 (Zea mays), 3'ss of exon 2
gtgaaggaggtttaagcattgatccatccaacttgtgaattat-tgcttctgtacattacttttctgtttccactg-tgtattcttacaacttccatgac-----agGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG
       |  ||| | |  || | |   || |    |  |    || || |||   |||  |||    | |||      || ||||  |   |   | ||     ||||||||| ||| | ||||||||||| |||||||||||| |||  || ||||  || |||||| |   |
-------aatttttatctatgttgctagcaccagaggcctagcatgattgtgtttcttaggtttgaaatgccatgaacttactcttttattctgtctaaccttgcagGTTGGGTGAATCGCTTTGCCAATGCCGGTGATACTGCTGTGGTTGTTGCTGAGAACACAGCAGTTAAG

upper sequence: GLYMA09G24630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G25680.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgaaggaggtttaagcattgatccatccaacttgtgaattattgc-ttctgtacattacttttctgtttccactgtgtattcttacaacttccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG
|| |||    |||     |||    |||     ||||  |   ||  || |||     |   || |||  |  || ||  ||||      |  | | ||||||||||||||| | ||||| |||||||| || || ||  |||||||||| ||||| |||||| | |||
gtaaagccatttt-----ttggga-atctggtgtgtgtgtgtgtgtgttttgtcttcaaggcttatgtgacggct-tgggttctg-----tctcttaacagGTTGGGTTAATCGCTTTGCTAATGCTGGGGACACAGCCTTGGAAGTGGCAGGAAACACAGCAATGCGG

upper sequence: GLYMA09G24630.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g01050.t01 (Vitis vinifera), 3'ss of exon 2
----gtgaaggaggtttaagcattgatccatccaacttgtgaattattg-cttctgtacattacttttctgtttccactgtgtattcttacaacttccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG
      |  | |||  | | |  | || | |  |   | | |||  ||| ||| |  |    |  |   ||||     |    |||||| |   |||  | ||||||||||| ||  |||| ||||||||||||||| |||| |||||||| || |||||||||||||| |||
acaaaagtggtaggccttatctgttatacctttagaat-taaatagttgacttttaaagggaaaataattgttaatttta-aaattcttcc---ttctgttacagGTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAGGAAATACAGCATTGCGG

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|6341710|gb|AW164596.1|AW164596
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|192318263|gb|FK005795.1|FK005795
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|120495740|gb|EH223907.1|EH223907
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|151395908|gb|EV265785.1|EV265785
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|15812897|gb|BI785172.1|BI785172
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|14258831|gb|BG881739.1|BG881739
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|31456764|gb|CD398792.1|CD398792
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCCATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|254331920|gb|GR843663.1|GR843663
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|9565795|gb|BE475304.1|BE475304
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|192318264|gb|FK005796.1|FK005796
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|16342588|gb|BI968183.1|BI968183
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|120495594|gb|EH223761.1|EH223761
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTG
EST: gi|208142871|gb|GD942379.1|GD942379
EST:     TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAG                         GTTGGGTTAATAG
genomic: TCACTTCTGTGATGAATTCTGTGAAAGACTTGGTGTACCAAAACTTCCAGgtaaacatgt ... tccatgacagGTTGGGTTAATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgtacattacttttctgtttccactgtgtattcttacaacttccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG
                                  ttcttac  putative branch site (score: 2)
                                           cttccat  putative PPT
         attactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaggaggtttaagcattgatccatccaacttgtgaattattgcttctgtacattacttttctgtttccactgtgtattcttacaacttccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA