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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattgctatgtttagcttcttaagaaatgctctctcttgttattgtatttttggttcttttattcatgaatatgatgtccatatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA

Basic information

species Glycine max
transcript GLYMA02G42560.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 10
------------------------tgattgctatgtt----tagcttc--ttaagaaatgctctctcttgttattgtatttttggttcttttattcatg---aatatgatgtcca---tatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
                        |  |||  ||| |     |  | |  || |    || |  || |  |  || |||   |||    | | ||| ||    |||||||  | |   || |  || | ||| ||||| ||| || | ||||| ||| ||||||| ||||||||||| |||||||| || ||| | || || |||||||| |||||  | || ||||||||||| |
gtaagttccattacttctatgcttttgttgtgatgctgttacaattgcaatttacgcttgttacctatgctggttttatcagtggcatatattttcctgcaagatatgatagcgagtttaatgttttatattgcagGTTGTGCAAAGGTTTCAAGAATTGTTTGCACAAACAAAATACAAGGAAGCAGCTGAGTTGGCTGCAGAATCTCCTCAAGGTCTTCTCCGAACTCCTGATA

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 10
------------------------tgattgctatgt--ttagcttcttaagaaatgctc----tctcttgttattgtatttttggttcttttattcatg---aatatgatgtcca---tatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
                        |  |||  |||   |||   ||  ||   | |||      || |  |  || |||   |||    | | ||| ||    |||||||  | |   || |  || | ||| ||||| ||| || | ||||| ||| ||||||| ||||||||||| |||||||| || ||| | || || |||||||| |||||  | || ||||||||||| |
gtaagttccattacttctatgcttttgttgtgatgctgttacaatcgcaatttacgcttgttacctatgctggttttatcagtggcatatattttcctgcaagatatgatagcgagtttaatgctttatattgcagGTTGTGCAAAGGTTTCAAGAATTGTTTGCACAAACAAAATACAAGGAAGCAGCTGAGTTGGCTGCAGAATCTCCTCAAGGTCTTCTCCGAACTCCTGAGA

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 8
tgattgctatgtttagcttcttaagaaatgctctctctt-gttattgtatttttggttcttttattcatgaatatgatgtccatatttgt-tgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
   |    ||| ||   ||  |   |  |||   || |  ||  ||  | || |     |  |||| |  |   |    || |  | ||  |   | | ||||| ||| || | || || ||||||||||| ||||||||||| |||||||| || ||||| || || || ||||| || ||  || |  | |||||||| |
--ctaatgatgctttattttgtggaagttgcatactatgagtagttagacttctatggttaatattgaatagagtttcatcaaattatgaattgtactgcagGTTGTGCAAAGGTTCCAGGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAA

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
--------tgattgctatg--tttagcttcttaagaaatgctctctcttgttattgtatttttggttc-----------ttttattcatgaatatgatgtc---catatt-tgtt--gacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
        || ||   |||  | |    |||     ||     | | | ||| ||  ||    | ||            | | |||    | | ||| ||    |||||| || |  ||  ||  |||| ||  | || || || ||  |||| || |||||||| || ||||| ||||| |||||||| ||||||||||| |||||||| ||  | || ||||| |
gtatgcgatgtttatcatggatctgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 10
------tgattgctatgtttagcttcttaagaaatgctctctcttgttattgtatttttggttcttttattcatgaatatgatgtccatatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
      |  |   |||  | | || |||   | |        |   ||  |  | ||    |||||      | |    | || | || ||||  |||  |||||||| ||  | || || || ||  | ||||| |||||||| || ||||| ||||| |||||||| ||||||||||| || || || || || || ||||| |
aacacttagtaaatatcataaactcctt---agacctctaaacccattgctcgaattacatttcttaatgcaaagttcctcatattca-attt--tgatgttacagGTTGTCCAGCGGTTCCAAGAGTTATTTGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAGGGCATTCTACGGACACCTGATA

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
tgattgctatgtttagcttcttaa--gaaatgctctctcttgttattgtatttt-tggttcttttattcatg-aatatgatgtccatatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
  |     ||||||    |  | |  |      | | |  |||||    ||| | | ||  ||  ||   || ||| ||||  ||     | |  | ||  ||||| ||  | ||||| || ||| ||||||| || ||||| |||||||| ||||| |||||||| |||||||||||||||||||| || || || || ||||
--agaatcatgtttcatatagtcatggtggaaatttatactgttaaatcattatgtagtctttgcatatttggaatctgatagcctgccatttctatat--cagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 10
tgattgctatgtttagcttcttaagaaatgctctctcttgttattgtatttttggttcttttattca-tgaatatgatgtccatatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
| |     | || ||     | |   |  |        | |||    | | |   ||     | | |    ||  ||||   |   ||      |   ||||| ||  |||||||||| ||  | ||  | || |  || ||||||||||| ||||| |||||||| || || || ||||| |||||||||||||| || |
taaccaa-acgtataatgattgagttagaggaaaagactattaggaaagtctgatttggcacactgaacttattcgatggtaacggttaccttgaaaccagGTTGTACAACGTTTTCAAGAGTTATTCTCTCAGATGAAGTATAAGGAAGCAGCAGACCTTGCAGCGGAGTCGCCTCAAGGCATCCTTCGAACTCCAGATA

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 11
tgattgctatgttta-gcttcttaagaaatgctctctcttgt-tattgtatttttggttcttttattcatgaatatgatgtccatatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
| | |   |  | || |  |  ||    ||  | ||| |||| ||||      |     ||  ||  |   |  || |    | |   ||||||  ||  |||| ||| ||||||| || ||  ||||| | ||||  ||||| |||||||| || || |||||||||||||| ||| ||||||| ||||||||||| || |
tcagtataacttgtatgacttctatttcattttttcttttgtctattactgcatctaacctcatacactgaagaataagagactttggtgttgagttt--agGTTGTGCAACGTTTCCACGAGTTGTTTTCTCAAATGAAATACAAGGAAGCAGCTGACCTTGCAGCTGAATCACCAAAAGGAATACTTCGAACTCCAGATA

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 10
tgattgctatgtttagcttcttaagaaatgctctctcttgttattgtatttttggttcttttattcatgaatatgatgtccatatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
                        | || ||| |    |   ||  | ||| |   | |  ||    | | | |   || | ||| ||          |||| ||| |||| ||||| ||  | ||    ||||  || || || |||||||| |||||||||||||| || || |||||||||||||| || | |||||
------------------------gtaacgcttttatcttcgatgatctttct--ctttgctacctcttactgtatcgttc-tatgtga-------gtagGTTGTGCAACGGTTTCAGGAGTTATTCCAACAAATGAAGTACAAAGAAGCTGCGGAGCTTGCAGCTGAGTCCCCTCAAGGAATCCTTCGCACGCATGACA

upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 10
tgattgctatgtttagcttcttaagaaatgctctctcttgttattgtatttttggttcttttattcatgaatatgatgt-ccatatttgttgacatta-cagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
                                     |     || ||| || | |  | ||  || |   ||     | |  |||   |  |  | |  |||| ||| |||| ||||| ||  | ||    ||||  || || || |||||||| |||||||||||||| || || |||||||||||||| || | |||||
------------------------------------gtaacccttttatcttcgatgatctttctctttgctacctcttactgtatcgttctatgtgagtagGTTGTGCAACGGTTTCAGGAGTTATTCCAACAAATGAAGTACAAAGAAGCTGCGGAGCTTGCAGCTGAGTCCCCTCAAGGAATCCTTCGCACGCATGACA

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|193697299|gb|FK636159.1|FK636159
EST:     TAGCAGTTAGTCTTGCCAAAAGAGGAAATCTTCCTGGTGCTGAAAAGCTG                         GTAGTGGAACGTTTTCA
genomic: TAGCAGTTAGTCTTGCCAAAAGAGGAAATCTTCCTGGTGCTGAGAAGCTGgtatgtcaat ... gacattacagGTAGTGGAACGTTTTCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatttttggttcttttattcatgaatatgatgtccatatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
                                         tgttgac  putative branch site (score: 3)
             ttttattcatgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattgctatgtttagcttcttaagaaatgctctctcttgttattgtatttttggttcttttattcatgaatatgatgtccatatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
tgattgc
- - - - - - - -gcttctt
- - - - - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtc