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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattcttcagaaccataatatgatctcgaatttgacataattgttgttcatgtggatagaagctgacgatgcaatgatttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG

Basic information

species Glycine max
transcript GLYMA13G19280.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 1
tattcttcagaaccataatatgatctcgaatttgacataattgt-tgttcatgtggatagaagc--tgacgatgcaatga-tttatgtatt---ttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
        |  |   |  |||||||    |  ||||  ||  ||   | ||||||| ||| |    | | | |  |   |  ||    | |   |   | ||  |||||||| ||||| || ||  || | ||||||||||||||||| ||||| ||||| ||||| || ||||| ||||| |||||||| ||||||||||||||||
-------tatcattttcttatgatcgaataagtgactcaaccgtacatccatgtggctagtaattttaatgctctagcaagcttgctcactaaatccctatttccagGTTCTGTCTGTGGTCGGAATTTTGCAAGATGAAGTTGATCCTATGGTTTCTGTGATGAAAGTGGAGAAAGCTCCGCTGGAATCCTATGCTGACATTGGTG

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 1
-tattcttcagaaccataatatgatctcgaatttgacataattgttgttcatg-tggatagaagctgacgatg-caatgatttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
 |  |   ||  |      | |  | |  || |||   | ||  |  ||  |  | |  ||||| |    ||  | |   || ||  ||  ||| ||   |||||||| ||||| |||||  || | |||||||| ||||| || ||||| ||||||||||| ||||| ||||| ||| |||| |||||||| ||||| ||||
cttataaccaatagttggctctactattaaacttgctcttatgctcttttttacttgtgagaagttttttataaccaaacttgataaatcatttctt---cagGTTCTCTCTGTGGTTGGAATTTTGCAAGATGAGGTTGACCCTATGGTTTCTGTCATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCGGACATCGGTG

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 1
tattcttcagaaccata-atatgatctcgaatttgacataattgttgttcatgtggatagaagctgacgatgcaat--gatttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
   | |   | |    | ||    |   | |      | || || |        | |    ||||     |   |    |    |  | | |||  |  ||||||||||||||| |||||  |  | ||||||||||||||||| ||||| ||||| ||||| |||||||| || ||| ||||||||||||||||||||||||
---tttgttgcattgcacatgcattagtggaccgtttacaactggtaggggatagcaagccagcttgttttctcactcaaacagtcaaatgtttactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCACCTTTGGAATCTTATGCTGACATTGGTG

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 1
tattcttcagaaccataatatg---atctcgaatttgacataattgttgttcatgtggatagaagctgacgatgcaatgatttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
| | ||  | ||||||    ||   ||  |    || |    |||||| |     |    ||| | | |   ||   |   | |   |  | ||   | ||||||||| ||||| |||||  |  | ||||||||||||||||| ||||| ||||| ||||| |||||||| || ||| ||||||||||||||||||||||||
tgtgctcaataaccatttgttgtaaattgcacgctttagtggattgttttgaccatcaggagaggttcatcttgt--ttgctcactcaaatgttcact-tcagGTTCTCTCTGTGGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCGCCTTTGGAATCTTATGCTGACATTGGTG

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 1
--tattcttcagaaccataatatgatctcgaatttgacataattgttgttcatgtggatagaagctgacgatgcaatgatttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
   ||   |      | | |  |||| |    | ||   ||  |||  ||| |     |  | ||| |    | ||  |  |  |     | |||   | ||||||| || || |||||  || | ||||| ||||||||||| ||||| ||||| ||||| ||||| ||||| ||| |||| |||||||||||||||||||
aaaatcaatgctgctcctcaagtgatgtactctgtgtttta--tgtacttccttgatttgaatgcttatttagtaaacagcttggccaaatgtttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCTGTGATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCTGACATTGGTG

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
tattcttcagaaccataatatgatctcgaatttgacataattgttgttcatgtggatagaagctgacgatgca-atgat-ttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
                       | | || ||| |||    | ||           | ||| |      |  |  |||| || | |||| ||||| |   |||| || |||||||||||| |||||||||||||||| ||||||||||| ||||| ||||| || |||||||||||| |||| || |||||||||||||| |
----------------------gtattgagttttacaatgctcttccatggaaacgttgaaccaattcttctatgtgatattttttattatttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 1
tattcttcagaaccataatatgatctcgaatttgacataattgttgttcatgtggatagaagctgacgatgcaatgatttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
   | |    ||  |   | | |     |  |||   |  ||||  ||    | |   |  | ||  |||  |  |  ||    |||| |||| | | ||||||| |||||||||||| |||| ||||||||||| ||||||||||| ||||| ||||| |||||||| |||||| |||| || |||||||| ||||| |
--gtatgtgaaattagggtttaag---aatcttgtttttgttgtgattacgattgtgtgttgttgtggattta--gggttgctgatttgttttatgttagGTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTTGAGAAAGCTCCTTTGGAGTCATATGCTGATATTGGAG

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 1
tattcttcagaaccata-atatgatctcgaatttgacataattgttgttcatgtggatagaagctgacgatgcaatgatttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
| |  || | |   ||  ||      ||  |||  | ||     |  ||||     ||||   | |  | | |  |   |||  |  |  | | |  ||||||||||||||||||||| ||||| ||||| ||||||||||||||||| || || ||||| ||||||||||||||  ||||||| ||||||||||| || |
tctgttttatagttatgcattcttattcacattgaagatgtagttccttcaccatcatagtttcaggaggttct-tatattactttgtgctgtctcgtcagGTTCTTTCTGTTGTTGGTCTTCTCCAAGACGAAGTTGATCCAATGGTGTCCGTAATGAAAGTTGAGAAGGCTCCATTGGAATCATATGCTGACATAGGAG

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 1
tattcttcagaaccataatatgatctcgaatttgacataattgttgttcatgtggatagaagctgacgatgcaatgatttatgtattttttttt----tat-cagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
      | |||   |     |  ||  |     | ||  |   | |||   ||    |  || | | |    | |  |  |     |||| |||    | | ||||| ||||| ||||| ||  | || |||||||| || || |||||||| ||||| ||||| ||||| || |||||||| || || ||||||||||||||||
---aagttagagtaactgattagtcctgg--cggtcacgaacatggtttgagttatcaccagatcatgggaaacttgtccaaacgattttctttgtcttgtgcagGTCCTTTCAGTTGTGGGATTGCTGCAAGATGACGTGGACCCAATGGTTTCTGTTATGAAAGTTGAAAAAGCTCCTCTAGAGTCATATGCTGACATTGGTG

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 1
----tattcttcagaaccataatatg--atctcgaatttgacataattgttgttcatgtggatagaagctgacgatgcaatgatttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
    ||| ||| |  |   | |  ||  | |  |  | |  |||||    |  |    |    || ||||   | || || || |  || | || | |     |||||  | || || || ||| | || |||||||| || || || ||||| ||||| |||||||| ||||||||||| || || ||||||||||| || ||||
gaactatgcttgattaagctgacttggaaacctggctgtatcataaaccataattgcttttggagcagct--tgttgaaacgagtgttgaacttctgtg----cagGTCTTATCAGTGGTGGGGTTACTGCAAGATGATGTGGACCCTATGGTATCTGTAATGAAGGTAGAGAAGGCTCCACTAGAGTCTTATGCTGATATAGGTG

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|298176105|gb|HO015510.1|HO015510
EST:     TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAG                         GTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGAT
genomic: TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGAT
EST: gi|254325090|gb|GR834515.1|GR834515
EST:     TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAG                         GTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|209715035|gb|BW650886.1|BW650886
EST:     TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAG                         GTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|207775739|gb|GD749060.1|GD749060
EST:     TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAG                         GTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATACCAAATAGGTC
genomic: TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGAT-CCAA-T-GGTC
EST: gi|6482143|gb|AW201414.1|AW201414
EST:     TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAG                         GTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|17022246|gb|BM093280.1|BM093280
EST:     TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAG                         GTTCTTTCTGTTGTTGGG
genomic: TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGG
EST: gi|193492877|gb|FK459585.1|FK459585
EST:     TCGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAG                         GTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: T-GATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|13791396|gb|BG653987.1|BG653987
EST:     TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAG                         GTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|8284625|gb|BE022184.1|BE022184
EST:     TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAG                         GTTCTGTCTGATGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTC
genomic: TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTC
EST: gi|10234966|gb|BE803854.1|BE803854
EST:     TTGATAAGGATCAGTTGGAGCCTGGATGTGCTATTTTGATGCATAATAAG                         GTTCTGTCTGTTGTTGGGCTTCTGCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|5606209|gb|AI900307.1|AI900307
EST:     TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAG                         GCTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|17152958|gb|BM142891.1|BM142891
EST:     TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAG                         GTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttactta ... tttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcatgtggatagaagctgacgatgcaatgatttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG
               agctgac  putative branch site (score: 3)
                                      tattttttttttatc  putative PPT
                       atgcaatgatttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattcttcagaaccataatatgatctcgaatttgacataattgttgttcatgtggatagaagctgacgatgcaatgatttatgtattttttttttatcagGTTCTTTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTCATGAAGGTTGAGAAGGCTCCTCTGGAATCTTATGCTGACATTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - -tcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaatg