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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gataattggtattttggggatttgctgattatcttaattgcataaactgcatactgtcttgtgtacttttgtaaatgttagatttcttttgttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG

Basic information

species Glycine max
transcript GLYMA03G42370.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 2
gataattggtattttggggatttgctgattatcttaattgca-------ta-aactgcatactgtcttgtgtacttttgtaa-atgttagattt--cttttgttg--ttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG
  |   || |  |       ||||||  | |  |||| |  |       || |  ||| | |  | ||      |  || || ||| |    |   || ||  ||  ||| ||| || || |||||||| ||||| |||||| |||| ||||||||||| ||||| || ||||| || ||||||||||||||||| || || |||
-gtgtgtgctcgtcaaattctttgcttctcaatttaaatataactgtgctacaggtgcttgcgctattccaacttgctgcaacatgctcatctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 2
-----gataattggtattttggggatttgctgattatcttaattgcataaactgcatactgtcttgtgtacttttgtaaatgttagatttcttttgttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG
     | |   || | || ||    ||  | | || | |||||   |  ||   | |  ||  |   | |    || | ||||    ||  | |  |   || |||||| |||||||||||||| || |||||| |||| |||||||||||| | ||||| |||||||| |||||||| || || || ||  | || 
attttgttctatgttgttctgcaatttatcagtttgttttaatgctaggaaggtccttttgaatca-gcatacctg-agatgt---gttcttatactaaatgcagGTATAAAGGAGTCTGATACAGGGTTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAACAGATGATGCAAGAAGAACAACCGTTACAA

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 2
gataattggtattttggggatttgctgattatct-taattgcataaactgcatactgtcttgtgtacttttgtaaatgttagatttctt--ttgttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG
   | ||     |     | | | |   | |||      |  | |   |    |    ||| || | |    ||  ||  |  |  | |  |  ||   | ||| || |||||||||||||| ||  ||||| |||| |||||||||||| | ||||| ||||| || |||||||| || || || ||  | || 
---agttctctatcaaatgttcttccattcatcagctgctttaaaggttaagaaggtccttttgaattagcatacctgagatgtgccctcatacttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------------------------------------------------gataattggtattttg-gggatttgctgattatcttaat-tgcataaactgcatactgt--cttgtgta---cttttgtaaatgttag----atttcttttgttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG
                                                                                        ||       || |  | ||  |  |||| | ||     || || |   ||  | | |  ||||  ||   |||    ||||  |||      || |  | || |   |||||||||||| ||||||||||| || ||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||
gtatgtttcttattcgtgatatttccaatgtatagtgctatttgataaactgggcatgtattatgttgatccatgttgaaaatagtagtagccaaggttatatgagaagttttgataaactaggcatgtattatgggctgattatggcttgaataacacttcatgaaattatagcaatgattttcatcttataacagGTATCAAGGAATCTGATACTGGCTTAGCTGCACCAAGTCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 2
gataattggtattttggggatttgctgattatcttaattgcataaactgcatactgtcttgtgtacttttgtaaatgttagatttcttttgttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG
                                                       ||    ||   | |||     | |   ||     || | ||  ||| ||||||||||| || |||||| | || || || |||||||||||||| || |||||||| ||||||||||| || |||||||| || || 
-------------------------------------------------------gtgcgttgcgatcttgctgg-gcttttttgagcgtgcttttccagGGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAA

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ13722 (Selaginella moellendorffii), 3'ss of exon 2
gataattggtattttggggatttgctgattatcttaattgcataaactgcatactgtcttgtgtacttttgtaaatgttagatttcttttgttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG
                                                       ||    ||   |||||     | |   ||     || | ||  ||| ||||||||||| || |||||| | || || || |||||||||||||| || |||||||| ||||||||||| || |||||||| || || 
-------------------------------------------------------gtgcgttgcgattttgctgg-gcttttttgagcgtgcttttccagGGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAA

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|192301329|gb|FG990219.1|FG990219
EST:     NGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTG                         GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
genomic: AGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTGgtatgtgtga ... gttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|213602675|gb|DB956611.1|DB956611
EST:     NGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTG                         GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
genomic: AGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTGgtatgtgtga ... gttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|213589227|gb|DB957759.1|DB957759
EST:     NGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTG                         GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
genomic: AGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTGgtatgtgtga ... gttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|151405667|gb|EV275481.1|EV275481
EST:     NGCCGAGAAGGAGATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTG                         GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
genomic: AGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTGgtatgtgtga ... gttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|209702899|gb|BW667434.1|BW667434
EST:     NGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTG                         GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
genomic: AGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTGgtatgtgtga ... gttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|208155594|gb|GD951999.1|GD951999
EST:     CAAAAAAGGTCAATGATTTATGTG                         GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
genomic: CAAAAAAGGTCAATGATTTATGTGgtatgtgtga ... gttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|208228908|gb|GE024272.1|GE024272
EST:     AAAAGGTCAATGATTTATGTG                         GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
genomic: AAAAGGTCAATGATTTATGTGgtatgtgtga ... gttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|193409954|gb|FK370747.1|FK370747
EST:     -GCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTG                         GTATCAAGGAGTCTGATACT
genomic: AGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTGgtatgtgtga ... gttgttgtagGTATCAAGGAGTCTGATACT
EST: gi|213600299|gb|DB970277.1|DB970277
EST:     NGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTG                         GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
genomic: AGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTGgtatgtgtga ... gttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|208196800|gb|GE001032.1|GE001032
EST:     AAAAGGTCAATGATTTATGTG                         GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
genomic: AAAAGGTCAATGATTTATGTGgtatgtgtga ... gttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
EST: gi|213611619|gb|DB969007.1|DB969007
EST:     NGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTG                         GTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG
genomic: AGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTGgtatgtgtga ... gttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgcatactgtcttgtgtacttttgtaaatgttagatttcttttgttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG
                                     tttcttttgttgtt  CT-rich tract
                     ttttgtaaatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gataattggtattttggggatttgctgattatcttaattgcataaactgcatactgtcttgtgtacttttgtaaatgttagatttcttttgttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG