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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattattagcacttgcagttgtatgctgagttctaattctacgtcgttcaatcaaatttgatgtgttgtgctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTT

Basic information

species Glycine max
transcript GLYMA20G33910.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 14
-----gtagattattagcact-tgcagttgtatgctgagttctaattcta------cgtcgttcaatcaaatttgatgtg-ttgtgctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTT
     |||  | ||     || |    || | ||| |  | ||| |   |      |  | ||  |    ||   || || || |  ||| || ||||||||| ||||| ||||| |||||||| |  ||  |||||||  | || ||||| |||||||| |||||||| |||||||||||||| |||||||||||
gtactgtatgtcatcgctgctattttattttctgcagtttactattagcagcatatcaccattgcagagcatcatatctgattctaatttacgtagGTGGTGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTT

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 14
---------------------gtagattattagca----------cttgcagt-tgtatgctgagttc-taattctacgtcgttcaatcaaatt----tgatgtg----ttgtgctttgc---gcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTT
                     |||||||  |  ||          |||| | | |   || | ||||   |  | | | |  ||    | || |    |||  ||     | ||| || |    ||||||| |||||||| |||||||||||||| |  ||| |||||||  | |  ||||| ||||||||||||||||| ||||| || ||||| || ||||||||
gtatgcagttgctccacttcagtagatttctttcaatatgttttccttgtaatgtacttgttcagtttgcatctttgcattattatgcccaagtatgctgacatgacatctttgcattacaatacagGTGGAGGTGTTGCACTTCTTTATGCATCAAAGGAGCTGGATAAATTGCCGACTGCTAACTTTGATCAAAAGATTGGTGTACAAATCATTCAGAATGCTTT

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 13
-------------------------------------------------------------------gtagattatta--gcacttgcagttgtat-gctgagttctaattctacgtcgt-tcaatc------aaatttgatgtgttgtgctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTT
                                                                      ||||  |   |||   | | |||| |   | | | || |||    || |  ||| |         | |  || | |  |  | |  ||||||||||||||||||||||| ||||||||||  ||| | |||||| | || || || || |||||||| ||||| ||||| || ||||| || ||||||||
gtaatgtatcaattaaaatttcatggggggggggtgtttatgctgatttcctgtgttatttgctcctactgattcctgttgcatcagtatttgtgttagttattcctgatttcctgttgcgtcagtatgcccgggagtcaatctttaattgtgtatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G111477_T01 (Zea mays), 3'ss of exon 2
--------------------------------gtagattattagcacttgcagttgtatgctgagttctaattctacgtcgttcaatcaaatttgatg------tgttgtgctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTT
                                | |  ||  |     || |  |||| |  |   | || ||     || |    |  |    ||||       | |  |  | |  ||||||||||||||||||||||| ||||||||||  ||| | |||||  | || || || ||||| ||||| ||||| ||||| || ||||| || ||||||||
gtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatctcctgttgcatcagtatgcctgatagtcatctttaattgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 12
gtagattattagcacttgcagttgtatgctgagttctaattctacgtcgttcaat-----caaatttgatgtgttgtgctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTT
|||  |   |  || |   ||    |  ||  | | || | |||    |||   |     | ||    |    |          ||||| || ||||| |||||||| || ||| | || |||||||| || |||| ||| ||||||||||| || ||||| ||||||||||| || || || || ||
gtatgtctcttccagtg--aggaagactctttgatatagtgctaaaaagtttgctatgtgctaaagaaacaaatcaaaacacttgcagGAGGAGGTGTGGCTCTTCTATACGCAGCAAGAGAGTTGGAAAAACTTCCAACAGCCAACTTTGACCAGAAGATTGGTGTCCAGATTATTCAGAACGCATT

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------gtagattatt-agcacttgcagttgtatgctgagt---tctaattctacgtcgttcaatcaaatttgatgtgttgtgctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTT
             ||||||| |  |   |  |   |    |||  ||    |||  |  | ||||    ||| || ||| |  |    ||  | |  ||||||||||||| |||||| | ||||| ||  | ||| |||| ||  |||||||||| |||||||| || ||||| || || || |||||||||||||||||
taaatttatatacgtagattttagaaggcacgtcatgaattgcgaagcccctctggtgtttcgtctggtaatgaattttcaatttgattgggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTT

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|15814111|gb|BI786386.1|BI786386
EST:     AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG                         GTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA
genomic: AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattatt ... ctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA
EST: gi|209725420|gb|BW658282.1|BW658282
EST:     AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG                         GTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA
genomic: AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattatt ... ctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA
EST: gi|16344877|gb|BI970472.1|BI970472
EST:     AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG                         GTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA
genomic: AGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattatt ... ctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagttctaattctacgtcgttcaatcaaatttgatgtgttgtgctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTT
                        aatcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagattattagcacttgcagttgtatgctgagttctaattctacgtcgttcaatcaaatttgatgtgttgtgctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA