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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgcatgcattaactttttagtatttagtaaaccaaaaaatgtttggtttttttattgaccttctcaaagtccctaatattttttcccctgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA

Basic information

species Glycine max
transcript GLYMA11G12080.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g50340.1 (Oryza sativa), 3'ss of exon 2
---gcttgcatgcattaactttttagtatttagtaaaccaaaaaatgtttggtttttttattgaccttctcaaagtccctaatattttttcccctgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
   ||| |  ||    |||     | ||| |    |  ||  |||    |  |    |  ||||  |  |  ||   |  ||| |  | |    | |   ||||||| ||||| |||||||| |||||| || | ||||||||||||||||| ||||| || ||||||||||| || || |||||||||||||| || || ||
attgctagactggccaaacacaaaactatatgcatatgcagcaaaccgctattgaggtatttgaattaatgtaa--tctaaatgtgctatttttt-tggacagACACGAAGGCTTGGGAAGTTGATACTTTGCGGGGACACATGAATAATGTGTCATGCGTGATGTTCCATGCTAAGCAAGACATCATTGTGTCCAACTCAGA

upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
gcttgcatgcattaactttttagtatttagtaaaccaaaaaatgtttggtttttttattgaccttctcaaagtccctaatattttttcccctgtttt----cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
  |    | |   |  ||  ||| | |    ||||   |  || |    |     ||||||  |  |  || |     |   |   |   || ||||    ||||||||||||| |||||||| |||||| || | || |||||||||||||| || || || ||||||||||| || || |||||||||||||| || || ||
--tattctactgcacattggtag-actggccaaacgctattatatgca-taccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA

upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g50350.1 (Oryza sativa), 3'ss of exon 2
gcttgcatgcattaactttttagtatttagtaaaccaaaaaatgtttggtttttttattgaccttctcaaagtccctaatattttttcccctgtttt-cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
||   | |   |    | |  |  ||| | |    | |  |   ||   || ||| |  |            | |    ||  | | |   | |||  ||||||||||||| |||||||| |||||| || | || ||||||||||| || || ||||| ||||||||||| || || |||||||| ||||| || || ||
gcaaactt-tgtggggtgtggaacattcacttccactatcaccattgcattatttaaagggataataggtgatgcaatctaaatgtgctgttttttgacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAACGTGTCCTGTGTGATGTTCCATGCAAAGCAAGACATCATAGTGTCCAACTCAGA

upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G010054_T01 (Zea mays), 3'ss of exon 2
gcttgcatgcattaactttttagtatttagtaaac--caaaaaatgtttggtttttttattgaccttctcaaagtccc-taatattt---tttcccctgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
  ||      || ||    |||||| |||| | |    |||||  || |   || |  |  ||  |  |  || | |  |||| | |   | | |  | |   |||| |||||||| |||||||| |||||| | || || |||||||||||||| || ||||| ||||||||||| || || |||||||| |||||||| || ||
--tttagcagatcaa----ttagtacttagcatatgtgaaaaagagtatacattctacaaggaaatgtttgaaatgcaataatctatatgtgttctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGCCACATGAATAATGTGTCTTGTGTGATGTTCCATGCGAAGCAAGACATCATCGTGTCAAACTCAGA

upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G149406_T01 (Zea mays), 3'ss of exon 2
gcttgcatgcattaactttttagtatttagtaaac--caaaaaatgtttggtttttttattgaccttctcaaagtccctaatattttttcccctgtttt----cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
       |    |      ||||||  ||| | |    ||| ||| | |   || |  |  ||  |  |   | | |   |  || | ||  || |||     |||| |||||||| |||||||| |||||| | || || ||| |||||||||| || ||||| ||||||||||| || || |||||||||||||| || || ||
------tttagctgttcaattagtacctagcatatgtgaaagaatatatacattctacaaggaaatatttggaatgcaataatttatgtctgctctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGTCACGTGAATAATGTGTCCTGTGTGATGTTCCATGCGAAGCAAGACATCATTGTGTCTAACTCAGA

upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G62020.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------gcttgcatgc-attaactttttagtat-ttagtaaaccaaaaa--------atgtttggtttttttattgaccttctcaa-----------agtccctaatattttttcccctgt----tttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
                                     ||  |||| || ||   |  |  || ||| | |    ||||        |||  |   |  ||   |||   ||  ||           |||   ||| || ||||   |  |    || |||| || || || ||||| ||||||||  || |||| || |||||||| ||||||| ||||||||||||||| ||||||||||| ||||| ||||| |||||
gtaattatttggtggtatacttttgtgcttacaatttttatatgctatcaatcgtcaatgatgttactgatatgaaaatattctgcatgccttaatccttagatgaatctcgaaattgcaaagacgagttggtaacatgtttttaacgatatcattgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGCCATATGAATAACGTTTCATCTGTTATGTTCCATGCAAAACAGGACATAATTGTATCAAACTCTGA

upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
gcttgcatgcattaactttttagtatttagtaaaccaaaaaatgtttggtttttttattgaccttctcaaagtccctaatattttttcccctgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
    | ||   |||    | |  | | |  |    || | || |||      ||||||  | | |     ||   || ||   |||     |  || |||| || || || ||||| ||||||||  || |||| || |||||||| |||||||  |||||||||||||| ||||||||||| || |||||||| |||||
----gtatttcttatggatatc-tgtcttcttcttcacagaaagttaa----ttttatgaatcatt---gaggtactgatgcgtttcaattttgttgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA

upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g13430.t01 (Vitis vinifera), 3'ss of exon 3
gcttgcatgcattaactttttagtatttagtaaaccaaaaaatgtttggttttttta---ttgaccttctcaaagtccctaatattttttcccctgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
  || ||| ||||   ||  | ||||||  |       |   |  | |   ||| ||   |||| ||    || |      |  ||   |   ||  |||||||||| ||||| |||||||| |||||| |||| || |||||||||||||||||||||||  | || ||||| |  |||||  | |||||||||||||| ||
--tttcatccatttg-ttaatcgtattttctttttgttagggttatagaactttgtagaattgaactagctaatggtttgcaacttaccttttctactttcagACACAAAGGCTTGGGAAGTAGATACTTTGAGGGGGCACATGAATAATGTTTCATGTGTCTTCTTTCATGCAAGGCAGGATGTGATTGTGTCAAATTCAGA

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|208196880|gb|GE001056.1|GE001056
EST:     GATTGTCTCAGGAGCTGATGACCGACAAGTGAAACTTTGGAGGATGAATG                         ACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTT
genomic: GATTGTCTCAGGAGCTGATGACCGACAAGTGAAACTTTGGAGGATGAATGgtaaatatga ... ctgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTT
EST: gi|208118823|gb|GD918730.1|GD918730
EST:     GATGACCGACAAGTGAAACTTTGGAGGATGAATG                         ACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTT
genomic: GATGACCGACAAGTGAAACTTTGGAGGATGAATGgtaaatatga ... ctgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtttttttattgaccttctcaaagtccctaatattttttcccctgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
                                  tattttttcccctgtt  CT-rich tract
                               taatatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgcatgcattaactttttagtatttagtaaaccaaaaaatgtttggtttttttattgaccttctcaaagtccctaatattttttcccctgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA

- - gcatgca
- - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtccct