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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggtaacaccaacaaaaataatttgtaatgtttgtggataatgattatattataatctccactgttgtggtgacatactatatatgcatgtgtttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG

Basic information

species Glycine max
transcript GLYMA11G36810.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 10
-----tgggtaacaccaacaaaaataatttgtaatgtttgtggataatgattatattataatctccactgtt-gtggtgacata-ctatatatgcatgtgtttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG
     | |||   |  |         |  |   |  ||  |    |  || | | |  |  ||   |    |  |  |   ||  || |   |       ||| ||||||||| ||||||||||||||||||||||| |||||||| || |||||
gttggttggttgaattatttggttccaagtcggaaattactcatcatcgagtttgtggttctccttatgactcatattagtatttctgttggtttgaacattt-cagGTTTGATAGAAAACTGAAGAACACATATGACCACCTTCTTTTCAGCAG

upper sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 10
---------------tgggtaacaccaa--caaaaataatttgtaatgtttgt--ggataatgattatattataa----tctccactgttgtggtgacatactatatatgcatgtgt-ttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG
               |   |    |  |      |||    ||      ||||  |||| ||| || |      |    | ||    | | || ||| |   | | |     ||  |    ||||||||||||||||||||| ||||||||||| |||||||| || |||||
gttagttgattgaaatatttggttctgaactgtgaattgcctgattcccttgtctggattatgcttgttcgtcgagacatttctgaagctttgctgaaaatttctgttgttttgaatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG

upper sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 10
tgggtaacaccaacaaaa--ataatttgtaatgtttgtggataatgattatattataatctccactgttgtggtgacatactatatatgcatgtgt-ttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG
           |   |||   | || |    |||||     |    ||||| | | ||||   | |        | | ||     | || |    | ||||||||||||  |||||||||||||||||||||||||||| |||||||||||
--------gttagtgaaaccgttatctcccttgttttcttttggccattatgtgagaatcgagattacatgcaggtcttaactgctgtgaactaatattgcagGTTTGATCGAAAACTGAAGAACACATATGATCACCTACTCTTTAGCAG

upper sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 10
tgggtaacaccaacaaaaataatttgtaatgtttgtggataatgattata-ttataatctccactgttgtggtgacatactatatatgcatgt-gtttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG
|  ||          ||   |  || |||| |||||       | | ||| |||   | |   ||  | ||||    || | || ||  || | | ||||||||||||||| ||||||||||||||||| ||||| ||||| || |||||
ttagtc-tttgggtcaatgcatattttaatatttgtcttagtcgttgatagttaatgtgtttgctcat-tggtcctgtaatgtaaattaattttgattgcagGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG

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|51336354|gb|CO980220.1|CO980220
EST:     CAGAGACTGGATAAATTAGTTGGAGTCCCAGTCATAAATGTTCACATATG                         GTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG
genomic: CAGAGACTGGATAAATTAGTTGGAGTCCCAGTCATAAATGTTCACATATGgtaagtaatg ... gtgtttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG
EST: gi|151398360|gb|EV268231.1|EV268231
EST:     CAGAGACTGGATAAATTAGTTGGAGTCCCAGTCATAAATGTTCACATATG                         GTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG
genomic: CAGAGACTGGATAAATTAGTTGGAGTCCCAGTCATAAATGTTCACATATGgtaagtaatg ... gtgtttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG
EST: gi|12773974|gb|BG238901.1|BG238901
EST:     CAGAGACTGGATAAATTAGTTGGAGTCCCAGTCATAAATGTTCACATATG                         GTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG
genomic: CAGAGACTGGATAAATTAGTTGGAGTCCCAGTCATAAATGTTCACATATGgtaagtaatg ... gtgtttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatattataatctccactgttgtggtgacatactatatatgcatgtgtttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG
                              atactatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgggtaacaccaacaaaaataatttgtaatgtttgtggataatgattatattataatctccactgttgtggtgacatactatatatgcatgtgtttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - -ccaacaa
- - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcat