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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatcatgttgttcctgtgaccttaaattgttatgatttttattgcctctattgagaaattagacttgaatacttgtgaaatattgctgaatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG

Basic information

species Glycine max
transcript GLYMA13G19500.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 3
catatcatgttgttcctgtgaccttaaattgttatgatttttattgcctctattgagaaattagacttgaatac-ttgtgaaatattgctgaatcttg-cagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG
    |  | ||   | |   |||   ||||  |                  |  ||||    | |||  || |  |||||     || |||   |||| |||||  | || ||    |  || |||||||| ||||||||||||||||| | ||||||||| ||  ||
--gctggtatttcacattacaccaagaatttctcgaccaaaagaaaaaagaaaagagaggaaaaactctaacaaattgtgtctcttttctgtcacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATAGTG

upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G137930_T02 (Zea mays), 3'ss of exon 4
catatcatgttgttcctgtgaccttaaattgttatgatttttattgcctctattgagaaattagacttgaatacttgt-gaaatattgctgaatcttg---cagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG
|   |  |||    | |||  |  |      |     ||| |  ||| |   |  |    |||      || |||  | |||      |  | || |    |||||  | || |||   |  || |||||||| ||||||||||||||||| | ||||||||| || | |
ctgtttgtgtcacccatgttcctctgctccttggcactttctgatgcatgc-tcaaatgcttaag---aaagactcatagaagcgactcctattcctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATCAAG

upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 3
catatcatgttgttcctgtgaccttaaattgttatgatttttattgcctctattgagaaattagacttgaa--tacttgtgaa--atattgctgaatc-ttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG
   || |||||  ||   |||  |||       ||  | |   ||   ||| |||||| |||    | | |   | |    ||  |||  |  | ||  || |||||||| || ||||| ||||| |||||||||||||||||||| |||||||  || || || |||| |
--aatgatgttcatcgcctga--ttaggaaaccattttatgggtttaatct-ttgagatattgttgtgggaatcattaaccaagcatacggaggcattattacagGTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAG

upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 3
--------catatcatgttgttcctgtgaccttaaattgttatgatttttattgcctctattgagaaattagacttgaatacttgtgaaatattgctgaatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG
         || | |     ||    | |   ||||||||||  |   ||     |  | || |  ||  |   ||   || |||  | ||||  || | | ||||||||||| |||||||||||||| |||||||||||||||||||||||||| | ||||||||| || | |
actagtgaaatttgacaaaattttcataaa--taaattgttagaaaccttg----ccttcttaatcaaccaaggttct-tatttg-aacatatgtctaatttttgcagGTGGTTGAAATAGGGAAAGGGAGCAAGGTGAAATATGAACTTGACAAGAAAACTGGACTGATCAAG

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|298184004|gb|HO029217.1|HO029217
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|12489759|gb|BG043280.1|BG043280
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATANGGAAAGGAAGCAAGGTGAAATATTGAACTTGACAAA-G
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATAT-GAACTTGACAAAAG
EST: gi|26269126|gb|CA820189.1|CA820189
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|192330021|gb|FK020837.1|FK020837
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|13479768|gb|BG509111.1|BG509111
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|19346407|gb|BM891287.1|BM891287
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|37996937|gb|CF808526.1|CF808526
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|298181507|gb|HO022946.1|HO022946
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|298169347|gb|HO020707.1|HO020707
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|6133848|gb|AW132241.1|AW132241
EST:     GACCCCGAAGCT-CAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GA-CCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|9565429|gb|BE474938.1|BE474938
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|7587913|gb|AW703719.1|AW703719
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGANCAAA-G
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGA-CAAAAG
EST: gi|8403914|gb|BE059548.1|BE059548
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|192324146|gb|FK017877.1|FK017877
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|213593665|gb|DB971687.1|DB971687
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|209719745|gb|BW672120.1|BW672120
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|298178505|gb|HO024240.1|HO024240
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGC                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|209701982|gb|BW664582.1|BW664582
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
EST: gi|17154018|gb|BM143951.1|BM143951
EST:     GACCCGAAGCTCCAAAGATCTTCAACTGT                         GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA
genomic: GACCCGAAGCTCCAAAGATCTTCAACTGTgtaagcatat ... aatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctctattgagaaattagacttgaatacttgtgaaatattgctgaatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG
                                tgaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatcatgttgttcctgtgaccttaaattgttatgatttttattgcctctattgagaaattagacttgaatacttgtgaaatattgctgaatcttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC