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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actagtaattgaacaaatactattgttcttttttccccctttgcacgaatgttatttttctgtgggtttgtgtttactttgtgtaaactttctgtttcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG

Basic information

species Glycine max
transcript GLYMA10G26890.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G26890.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 3
actagtaattgaacaaatactattgttcttttttccccctttgcacgaatgttatttttctgtgggt---ttgtgtttactttgtgtaaactttctgtttc-------agGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG
           || |  |  || ||||     |   | ||     |     || ||| ||| |  ||   |||  |||  | ||  |||| ||  ||||||       ||||| |||||||||||  | ||||||||||||||||||||||||||||| || |||
----------aaatagcttgtactgtttaggatgttctctacaagcatgctttgtttctctttatgtattttgatttttgtctgactaaatttgttgtttcttttgccagGGCGTGCTATGGTGTGCTCAGGTTTGTTATGGAGAGTGGTGCTAAGGGCTGTGAG

upper sequence: GLYMA10G26890.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G093902_T02 (Zea mays), 3'ss of exon 3
actagtaattgaacaaatactattgttcttttttccccctttgcacgaat-gttatttttctgtgggtttgtgtttactttgtgtaaactttctgtt------tcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG
      |||||     |||   |||| |  | | | || ||||  |   | ||| ||  ||||     | || |||  |||    ||   || ||||      ||||||| || ||||||||| | |||||||| |||||||||||||||||||| || |||
------aattgttaggatatccttgt-cagtatgctccatttgttcaccttgtttttcctctgctatgtagtcttttatttactaaactgttttgttcgattttcagGGCATGTTATGGTGTTCTCAGGTTTGTCATGGAGAGTGGTGCTAAGGGCTGTGAG

upper sequence: GLYMA10G26890.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G53870.1 (Arabidopsis thaliana), 3'ss of exon 3
actagtaattgaacaaatactattgttcttttttccccctttgcacgaatgttatttttctgtgggtttgtgtttacttt--gtgtaaactttctgtttc----agGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG---------------------------------------------
    |||||||  |  |||  | | |   |  || |   |  | |    | |   || |  |||   |    || | ||    || ||   || | | |     ||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||||                                             
----gtaattgttcttatag-actctgtatggtttcaaataggtattg-tctagcttctaagtgtaatgactttaagttctcatgcaatggttatatgttgtatagGGCTTGCTATGGTGTGTTGAGGTTTGTTATGGAGAGTGGAGCTAAGGGATGCGAGGTTATCGTGAGTGGAAAGCTTCGTGCTGCCAGAGCCAAGTCTATG

upper sequence: GLYMA10G26890.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 3
-----actagtaattgaacaaatactattgttcttttttccccctttgcacgaatgttatttttctgtgggtttgtgtttactttgtgtaaactttctgtttcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG---------------------------------------------
     |||  | ||  |  |  |           | || |  |  ||     | |   | || ||       ||    || |  || ||| | ||  | |  ||||||||| |||||||||||||| ||||||||||||||||| ||||||||||| |||                                             
aacacactgatgatacataatgtgtcgacaaggctattgcatctcttttttcacttgaacttctcatc---cttaatattgcaatg-gtatatttgatata-cagGGCCTGTTATGGTGTTTTGAGATTTGTTATGGAGAGTGGAGCTAAGGGATGTGAGGTCATCGTGAGTGGAAAGCTCCGTGCTGCACGTGCTAAGTCCATG

upper sequence: GLYMA10G26890.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G35530.1 (Arabidopsis thaliana), 3'ss of exon 3
----actagtaattgaacaaatactattgttcttttttccccctttgcacgaatgttatttttctgtgggtttgtgtttactttgtgtaa-actttctgtttcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG
      || |  || ||     ||| || | ||   |    | |||   |     |   || |     |     |||| |  |||  | | | ||| |  |  ||||| |||||||||||||| |||||||||||||||||||| ||||| |||||||| 
ttatgttact--ttaaatttgaactgttctcctaaatatggcttttatgctttgatctcttatgctcaga---atgttaatattgcatgatattttgttgtatagGGCGTGCTATGGTGTTTTAAGGTTTGTTATGGAGAGTGGAGCTAAAGGATGCGAA

upper sequence: GLYMA10G26890.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g01380.t01 (Vitis vinifera), 3'ss of exon 3
----actagtaattga-acaaatactattgttcttttttccccctttgcacgaatgttatttttctgtgggtttgtgtttactttgtgtaaact-ttctgtttcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG
      ||  | |||  |||  ||  | |||   ||  || |  | ||    |  | | ||       | |      ||| | || ||    || | || ||| ||||||||||||||||||||||| ||  ||||||| ||||| || |||||||| |||
aagtgttaacacttgccacacttagcaatgtggattagtcacgatctgtttcatggctgttc------gagccctaatttgccttctggttgctgtcctattttagGGCCTGCTATGGTGTTTTGAGATTCATTATGGAAAGTGGGGCAAAGGGATGTGAG

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|298167771|gb|HO013034.1|HO013034
EST:     CAGGCTGAGTCTCTTCGCTACAAGCTCCTTGGTGGACTCGCTGTGCGCAG                         GGCCTGCTATGG
genomic: CAGGCTGAGTCTCTTCGCTACAAGCTCCTTGGTGGACTCGCTGTGCGCAGgtgtatattc ... tctgtttcagGGCCTGCTATGG
EST: gi|298195932|gb|HO044323.1|HO044323
EST:     CAGGCTGAGTCTCTTCGCTACAAGCTCCTTGGTGGACTCGCTGTGCGCAG                         GGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATG
genomic: CAGGCTGAGTCTCTTCGCTACAAGCTCCTTGGTGGACTCGCTGTGCGCAGgtgtatattc ... tctgtttcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATG
EST: gi|6726858|gb|AW311277.1|AW311277
EST:     CAGGCTGAGTCTCTTCGCTACAAGCTCCTTGGTGGACTCGCTGTGCGCAG                         GGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATG
genomic: CAGGCTGAGTCTCTTCGCTACAAGCTCCTTGGTGGACTCGCTGTGCGCAGgtgtatattc ... tctgtttcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATG
EST: gi|6725216|gb|AW309615.1|AW309615
EST:     CAGGCTGAGTCTCTTCGCTACAAGCTCCTTGGTGGACTCGCTGTGCGCAG                         GGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATG
genomic: CAGGCTGAGTCTCTTCGCTACAAGCTCCTTGGTGGACTCGCTGTGCGCAGgtgtatattc ... tctgtttcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaatgttatttttctgtgggtttgtgtttactttgtgtaaactttctgtttcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG
                                          ctttctgtttc  CT-rich tract
      ttatttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actagtaattgaacaaatactattgttcttttttccccctttgcacgaatgttatttttctgtgggtttgtgtttactttgtgtaaactttctgtttcagGGCCTGCTATGGTGTTTTGAGGTTTGTTATGGAGAGTGGTGCTAAGGGATGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - ttccccc
- - - - - - - - - - - - - - - - - - - - -tgcacga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttgtg