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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaactttgtaatgatgtaatgtagttctacatgatgactctctaaagggaattatcatgaaatttgattgaattagtaaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC

Basic information

species Glycine max
transcript GLYMA19G42850.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g06970.3 (Oryza sativa), 3'ss of exon 1
---gttaactttgtaatgatgtaatgtagttctacatgatgactctctaaagggaattatcatgaaatttgattgaattagtaaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC
      ||  |        | | |  |   | |   |  ||  |   ||     | |  |  |     |     || | |  | ||||   |||     | || |||||||||||||| ||||| || |  |||||||| || || ||||| || |||||||| || |||||||| ||||| |||||||||||||||||||| 
agcacaaatgtaactgctgtctgaattgcatatgtgtattgggttcttacctccactccttgtagtgctg---cgattaaccataatttctgttcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAAT

upper sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g19060.2 (Oryza sativa), 3'ss of exon 1
-----gttaactttgtaatgatgtaatgtagttctacatgatgactctctaaagggaattatcatgaaatttgattgaattagt-aaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC
       |||||    | |||  || |    ||||  ||  ||  ||  ||        |       | |       | |||   ||| ||   |||     | || ||||| |||||||| ||||| || |  |||||||| || || ||||| || |||||||| || |||||||| ||| | ||||||||||| |||||||| 
acaaatataactactcactgaaatatttgcattctttatattggttccttac------ctccaggccagtgctgcaaagttaaccaaagtttctgttcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT

upper sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G886989_T03 (Zea mays), 3'ss of exon 2
gttaactttgtaatgatgtaatgtagttctacatgatgactctctaaagggaattat-catgaaatttgattgaattagt-aaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC
   |  | ||| |   |    |||  || |   |  ||        ||       || |||| |  |     || | |   ||| || | |||  |  | || |||||||||||||| ||||| || |  |||||||| || || |||||||| |||||||| ||||||||||| ||||| |||||||||||||||||||| 
--cagatctgtcagttttctgtgtgattattttttttggtcagtgcaacactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT

upper sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G123807_T02 (Zea mays), 3'ss of exon 2
gttaactttgtaatgatgtaatgta-gttctacatgatgactctctaaagggaattat--catgaaatttgattgaattagtaaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC
   || | |||     | |  |||  | |  |  |  | | ||  |  |  |    |   |||| | ||     || | |   |  || || ||  |  | || |||||||||||||| || || || |  |||||||| || || ||||| || |||||||| || || ||||| ||||| |||||||| ||||||||||| 
--caaatctgtctcagttttctgtgtgattaatttttttagtcagtgcaatgctccaatgcatgtacttctgcagactcaaccattttttg-ttcatattcagATATACCATGGAGCGTCCACGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTCTGGTCAGAGCTGTTCAAGAAACAGATTGACAAT

upper sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
---gttaactttgtaatga-tgtaatgtagttctacatgatgactctctaaagggaattatcatgaaatttgattgaat-tag--taaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC
    ||  ||   |||  | |||  |  |||  |  |||||| |       ||  | ||| |||   | |||||||    ||   | |   | |  | ||| |||||||| || |||||  | ||  ||||||  || ||||| ||||| |||||||| |||||||| || || ||||||||| ||||||||||||||||||| || 
gtgtttgcctacataaaaactgttttacagtgttgtatgatggc-------agatatttagcattttacttgattgtgcataacttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT

upper sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0030g00700.t01 (Vitis vinifera), 3'ss of exon 1
gttaactttgtaatgatgtaatgtagttctaca--tgatgactctctaaagggaattatcatgaaatttgattgaattagtaaaattgtggtttgttgtt---agGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC
    |    || || || || | |||  | | |     |     ||         || |  |    | |  |   | || |||||  ||  ||| || ||   || ||||| |||||| |||| ||||| |  |||||||| ||||| |||||||| ||||||||||| || ||||||||||||||||||||||| || ||||||
----agggagtgatcatata-tatagccccataatccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtatttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC

upper sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ32385 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------------------------------------gttaactt-tgtaatgatgtaatgtagttctacatgatgactctctaaaggg-aattatcatgaaatttgattgaattagtaaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC
                                                                                            | |  |||  || |   |    | | | |  |  |  | | |  | || |   || | ||| |||  | | ||   |     |  || |    | ||   || || || |  || || || || ||||| || ||  | || | |||||||||||| ||||||||||| ||| | ||| | |||||||||||||||||||| 
gtaaaattttcttacattgccgtggagctcaaatgcttgcgaggaatgtggcttgcattccttgatctgcttagattggttccagtggatctgcttgcttgcgtgaattttccttttggattgatcttgtaagttccaaatgtataaatctcaagaaggt-ggttttttcttcgatcttttttcctctttccagATACACAAGAGATCGTCCGCGATTCACAGACCACTTGGAAGTCATCAAGTTCATATGCAAGGATTTCTGGGCGGAGGTTTTCAAGAAGCAGATTGACAAT

upper sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ20859 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------------------gttaactt-tgtaatgatgtaatgtagttctacatgatgactctctaaaggg-aattatcatgaaatttgattgaattagtaaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC
                                                                     | |  |||  || |   |    | | | |  |  |  | | |  | || |   || | ||| |||  | | ||   |     |  || |    | ||   || || || |  || || || || ||||| |||||  | || | |||||||||||| ||||||||||| ||| | ||| | |||||||||||||||||||| 
gtaaaattttctgctcaaatgcttgcgaggaatgtggcttgatctgcttagattggttccagtggatctgcttgcttgcgtgaattttccttttggattgatcttgtaagttccaaatgtataaatctcaagaaggt-ggttttttcttctatcttttttcctctttccagATACACAAGAGATCGTCCGCGATTCACAGATCACTTGGAAGTCATCAAGTTCATATGCAAGGATTTCTGGGCGGAGGTTTTCAAGAAGCAGATTGACAAT

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|31561880|gb|CD487718.1|CD487718
EST:     GGATATCAGGTCGGTCACCAGCTCTCTGAAAG                         GTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTT
genomic: GGATATCAGGTCGGTCACCAGCTCTCTGAAAGgttgtttcca ... ttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTT
EST: gi|22525870|gb|BU084681.1|BU084681
EST:     CGCAGGATCGAGGCCATTGGATATCAGGTCGGTCACCAGCTCTCTGAAAG                         GTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTT
genomic: CGCAGGATCGAGGCCATTGGATATCAGGTCGGTCACCAGCTCTCTGAAAGgttgtttcca ... ttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTT
EST: gi|192297826|gb|FG988324.1|FG988324
EST:     CGCAGGATCGAGGCCATTGGATATCAGGTCGGTCACCAGCTCTCTGAAAG                         GTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTT
genomic: CGCAGGATCGAGGCCATTGGATATCAGGTCGGTCACCAGCTCTCTGAAAGgttgtttcca ... ttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTT
EST: gi|24136644|gb|BU927154.1|BU927154
EST:     CGCAGGATCGAGGCCATTGGATATCAGGTCGGTCACCAGCTCTCTGAAAG                         GTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTT
genomic: CGCAGGATCGAGGCCATTGGATATCAGGTCGGTCACCAGCTCTCTGAAAGgttgtttcca ... ttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTT
EST: gi|51335698|gb|CO979564.1|CO979564
EST:     CGCAGGATCGAGGCCATTGGATATCAGGTCGGTCACCAGCTCTCTGAAAG                         GTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTT
genomic: CGCAGGATCGAGGCCATTGGATATCAGGTCGGTCACCAGCTCTCTGAAAGgttgtttcca ... ttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagggaattatcatgaaatttgattgaattagtaaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC
      aattatcatgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaactttgtaatgatgtaatgtagttctacatgatgactctctaaagggaattatcatgaaatttgattgaattagtaaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - -aatgtag
- - - - - - - - - - - - - - - - -tgatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaaa