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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG

Basic information

species Glycine max
transcript GLYMA09G01820.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG
                 | ||| |||       ||     || ||  |  | |  | |          ||| | || |   | || || | |   |||| ||  | ||     ||||||||||||| || ||||||||||| |||||||| |||||||| |||||||| ||||| || |||||||| ||||||||||| |||||  ||
----------------gtaatgttttctccaaatgctatcttgtaggatgtttgttagccaagtgaagtta-tatgcta--agtgtggcaccac-tgatggt--tctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG

upper sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g50050.1 (Oryza sativa), 3'ss of exon 3
gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG
                     |    |  |  ||| ||||||     |  |   ||  |   | |    || |   |    |||     | ||| |  | ||  ||||| |     ||||||||||||| |||||||| ||||||||||| || ||||||||||| || || || || ||  | || || ||||||||  | ||||||
---------------------gtacatgatacttgtatgatttagtgacctgggattatgaaacaacaatattagcaaaatattttctaaactttt--ttgttctttga-gtaacctgcagCTTCAGGCCTATTTTCTGGTTCTTGATGATATAATGGATAACTCACAAACTCGACGAGGAAAACCCTGTTGGTTTAGGCTTCCCAAG

upper sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 2
gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagat-gtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG
               |     | |  |  ||||||  |   | ||  | || ||||  |   |||| |  |  | || |    ||||  | |    | |   | | |||     | || |||||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| || |||||||| |||||||||||||||||  ||
---------------gtactagttccttctgtttgttt---tctatcatttttaatattaatagattgcattttctgctaat-ttggaattttaattcactatttcttg-----tcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG

upper sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 2
gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG
            |   ||||    | | ||| ||  | |  | |  || |  |||  |  | |  | | | ||   |||  |||      |   || |   | | ||      | ||||||||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| || ||||| || |||||||||||||||||  ||
----------gtactacttacttctgtgttgctttcaagcatttttta-tgttaacagaatgaattttctgctaatatgaaatt------ttaaatcactatttctta-----tcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG

upper sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G168681_T01 (Zea mays), 3'ss of exon 3
gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG
                    |  |||| || ||||        |  |      ||   |  |||    | |  |   ||  | |||   |||| | | |||    | |     | || ||||||||||| |  |||||||| |||||||| || |||||| |||||||||| || ||||||||||| |||||||| || |||||  ||
-------------------gtatttttttt-tttgtcccccactgttgccaggaaaaatgccag----tcaaggaactgagagtggctcatctaa-gttcgctcgtcg-----tatttcagCTTCAGGCTTTCTTTCTTGTGCTTGATGATATCATGGATGACTCTCACACTCGTCGCGGCCAGCCTTGCTGGTTCAGGGTGCCTCAG

upper sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
lower sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG-------------
                                           || |   |||  |   |||   | ||  || | ||  || ||    || || |        |||| | |  |||||||||||| || ||||| ||||| ||||||||||| ||||| ||||||  ||||||||| |||||||| || |||||||||  ||| |||             
------------------------------------------gtaattcctctt-ttacttctcttcttatctttcatctcaatgct-cattttgta-------tttgcttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG

upper sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG
   ||   | | | ||  ||||| ||||   | | | | |  | |||     |||  ||  |        |   | ||  |  ||        || || ||      || ||    ||||||||| || || ||||| ||||| |||||||| |||||||||||||||  ||| ||||| || || || |||||||| ||||| ||  ||
gtataccaatgataaagacttatcctttcaatctct-attagtaatagatactctcctctctct-----ctctttatgtcgctatca------ctcatcat-----attcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG

upper sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 3
gtatggaagttgaaagcttatgcttttcttgtt-----tgaatgattatactagttc--taatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG
||| | ||    | | ||      | | |||||     ||||   || |   || ||  ||||| |  |||    |  || |  | ||||   |  |  |||||      |||  |||    ||||||||||| |||||||| ||||| |||||||| |||||||||||||| || ||||| || || || || |||||||| || || ||||||
gtaggcaacagaatacctcccctgtattttgttaaggctgaagctttttctcaggtccataatcataccagtgtatcgcttttgttgcat---gacaatttatgccttcttttctatgccacttgcagCTTCAAGCATATTTCCTTGTGCTTGATGATATTATGGATAACTCGCATACACGTCGAGGTCAACCTTGCTGGTTCAGGGTTCCCAAG

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|13180801|gb|BG352141.1|BG352141
EST:     ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGGgtatggaagt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|192297466|gb|FG992694.1|FG992694
EST:     ATGATGACGAAATTTTCCTTGCTAATGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGGgtatggaagt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|193645084|gb|FK593384.1|FK593384
EST:     ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGGgtatggaagt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|8282987|gb|BE020548.1|BE020548
EST:     ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATG
genomic: ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGGgtatggaagt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATG
EST: gi|192325137|gb|FK017523.1|FK017523
EST:     ATGATGACGAAATTTTCCTCGCTAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGGgtatggaagt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|6567264|gb|AW234875.1|AW234875
EST:     ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGGgtatggaagt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|8826734|gb|BE210464.1|BE210464
EST:     ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGGgtatggaagt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|213591397|gb|DB973830.1|DB973830
EST:     ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTCCTTGCTAGTGCTCTTGGTTGGTGTATTGAATGGgtatggaagt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG
                                     ttttgat  putative branch site (score: 4)
                      tatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG