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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatatttagacatgcttagatatgtgtaggcttctttctgttgaaaaaaacaattatttaggcttccgcataagatgatttggtttgcctaatttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAAGAGCTGAGTCATGCTTTGTATCAG

Basic information

species Glycine max
transcript GLYMA20G21330.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G21330.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G037698_T01 (Zea mays), 3'ss of exon 4
-aaatattta-gacatgcttagatat--gtgtaggcttctttctgttgaaaaaaacaattatttaggcttccgcataagatgatttggtttgcctaatttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAAGAGCTGAGTCATGCTTTGTATCAG
 | | || |  || |  | |   |||   ||| | ||       | || |||  |  ||| | |||   ||  |   |  |  |||   |||  |  |||| |||| |||||||   | ||||| ||||||||||| |||||||| ||  | ||||||||||||||||| || ||||||||  | || |||
aatagatctgtgatacacatcattattactgtggcctgtccaaagatgcaaatcatgattctatag--ctctacccgaacttgtttttcttgaat--tttgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTACACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG

upper sequence: GLYMA20G21330.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G324540_T02 (Zea mays), 3'ss of exon 3
aaatatttagacatgcttagatatgtgtaggcttctttctgttgaaaaaaacaattatttaggcttccgca--taagatgatttggtttgcctaa--tttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAAGAGCTGAGTCATGCTTTGTATCAG
    ||  | |     ||  |||| |||    |   | ||||  |||      | |  | |  ||   ||   ||  |  | ||| ||| ||| |  || | |||| |||||||   | ||||| ||||||||||| |||||||| ||  | ||||||||||||||||| || ||||||||  | || |||
--tgatccatat-catttttatat-tgtcaattgtgtcctgtctaaagttttgagtcataattctctagctcttatcagaacttgtttttcctgaatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG

upper sequence: GLYMA20G21330.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G33340.2 (Arabidopsis thaliana), 3'ss of exon 4
-aaatatttagacatgcttagatatgtgtaggcttctttctgttgaaaaaaacaattatttaggcttccgcataagatgatttggt-ttgcctaatttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAAGAGCTGAGTCATGCTTTGTATCAG
      |||     |||| |   |  |  |   ||| || | |||  |  ||  ||  |  | |     || | ||| | || | |  |    | ||| ||||||||||| || ||||||||||| ||||||||| ||||||||||| | || || ||||| |||||||| |||||||| |||||||||
gctccttttctgagtgctaatcaacataaattgttcatttttttgggatgaattat--tcgaagtaattgcgtgagaagtttagctgctttgcattttttagGAATGGGACGGTTTGATGCTATCAAATTTTGCACTGGAGCAACAACTACATACTGCAAGGCAAGAGCTAAGTCATGCCTTGTATCAG

upper sequence: GLYMA20G21330.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G04510.2 (Arabidopsis thaliana), 3'ss of exon 4
-------aaatatt--tagacatgcttagatatgtgtaggct-tctttctgttgaaaaaaacaattatttaggcttccgcataagatgatttggtttgcctaatttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAAGAGCTGAGTCATGCTTTGTATCAG
          || |  |||  |  |  |  | |  |  || | | |||   ||    |||| || |  |||           ||| | || || ||||      ||||||||||||||  | ||||||||||| |||||||| ||||| |||||| |||| || || || |||||||| ||||| ||||||||||||
gttcatttgttactaatagcaagacgaaagtgttcgctggttatttttactttaggcaaaagaaatgcttaaa---------aagtttatctg-tttgttgtgcttgtagGAATGGGACAGTTTGATGCTATCAAATTTTGCTTTGGAACAACAACTGCATACTGCGAGGCAAGAGCTAAGTCACGCTTTGTATCAG

upper sequence: GLYMA20G21330.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0049g01840.t01 (Vitis vinifera), 3'ss of exon 4
aaatatttagacatgc--ttagatatgtgtaggcttctttctgttgaaaaaaacaattatttaggcttccgcataagatgatttggtttgcctaatttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAAGAGCTGAGTCATGCTTTGTATCAG
|  |  ||||  |||   |||||| ||       || ||  | || ||| |  |  | ||||     |          |  |||   ||    || |  |||||||||||||| ||||||||||| |||||||| |||||||||||| |||| || || || || ||||| |||||||||||||| |||
atgttgttagttatggcattagat-tgcacttcattgttaatttt-aaagattctctcattttaatatttaaggccttttttttttctttttcaaataatagGAATGGGATGGCTTGATGCTATCCAATTTTGCGTTGGAGCAACAACTGCATACTGCTAGGCAGGAGCTAAGTCATGCTTTGTACCAG

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|10238874|gb|BE807770.1|BE807770
EST:     GACCTGTTCAGGCAGCTAGCATCCCTGGCATGCTTGGAATGTTCCAAAAT                         GAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCAC
genomic: GACCTGTTCAGGCAGCTAGCATCCCTGGCATGCTTGGAATGTTCCAAAATgtatggaatt ... taatttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCAC
EST: gi|209719891|gb|BW665974.1|BW665974
EST:     GACCTGTTCAGGCAGCTAGCATCCCTGGCATGCTTGGAATGTTCCAAAAT                         GAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCAC
genomic: GACCTGTTCAGGCAGCTAGCATCCCTGGCATGCTTGGAATGTTCCAAAATgtatggaatt ... taatttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaacaattatttaggcttccgcataagatgatttggtttgcctaatttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAAGAGCTGAGTCATGCTTTGTATCAG
                                          gcctaat  putative branch site (score: 3)
                                       tttgcct  CT-rich tract
     acaattattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatatttagacatgcttagatatgtgtaggcttctttctgttgaaaaaaacaattatttaggcttccgcataagatgatttggtttgcctaatttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAAGAGCTGAGTCATGCTTTGTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - acatgct
- - - - - - - - - - -tatgtgt
- - - - - - - - - - - - - - - gcttctt
- - - - - - - - - - - - - - - - - - -tctgttg
- - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttgcc