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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acctttcacaatgcacctttcattttccacacttcattcacacaccaacaaacactgatacattttcgtaattcatttatttattgttttggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCAATTAAGCCAATAACTCATAAGCGTCTTATCGAAAAAGAGCTAGAGGGAT

Basic information

species Glycine max
transcript GLYMA04G39690.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 3'ss of exon 5
acctttcacaatgcac-ctttcattttccacacttcattcacacaccaacaaacactgatacattttcgta-attcatttatttattgttttggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCAATTAAGCCAATAACTCATAAGCGTCTTATCGAAAAAGAGCTAGAGGGAT
     | | | |  |  |  | |||   || | ||   |       ||  ||    || |   ||  | |  | ||   ||  ||   |    |   | |||||||| || || ||||| |||||||||  |||| ||||||| |||||||| |||||||||||||| || ||||| ||||| || || ||||| |||||||
--tagtaatattatatgcaataattaagcatatttttgttgtttgtcaggaagttatgctgttttcccttctagtctgatagatagcttacatgtttttcagGTTATCAGCACAGCAAGGACATGCAATGTCATTCTGATTGTTCTTGATGCCATTAAGCCAATAACCCACAAGCGGCTTATTGAGAAGGAGCTTGAGGGAT

upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 5
--acctttcacaatgcacctttcattttccacacttcattcacacaccaacaaacactgatacattttcgtaattcatttatttattgttttggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCAATTAAGCCAATAACTCATAAGCGTCTTATCGAAAAAGAGCTAGAGGGAT
  ||  ||||   |     |||| | |   |  |    |||         |  | ||   | | | || |   |  |  |   |||| || |||     |||||||| || || || || |||||||||   ||||||||||| |||||||| || || ||||||||||| ||||||||||| || || ||||| || ||||
taacacttcagtcttggattttcttgtgttattccgtgttctt-tgtgtgcgga-accatttcttcttgggcttgaaagttcctatttttgtggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGAT

upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 5
acctttcacaatgcacctttcattttccacacttcattcacacaccaacaaacactgatacattttcgtaattcatttatttattgttttggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCAATTAAGCCAATAACTCATAAGCGTCTTATCGAAAAAGAGCTAGAGGGAT
         ||  |   | | | | ||   | |   || | |     ||   |  ||||    ||||  | ||        || | |||        |||||||| ||||| || || |||||||| ||||| || || || |||||||| || || ||||| ||||| |||||||| || ||||||||||| || ||||
-------gtaagtcgagtctaaatctcttgagtat-tttatattttgaccctctttgatcatctttcacactt--------tactatttc-------cagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGAT

upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0031g01620.t01 (Vitis vinifera), 3'ss of exon 5
acctttcacaatgcacctttcattttccacacttcattcacacaccaac---aaacactgatacatttt-cgtaattcatttatttat--tgttttggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCAATTAAGCCAATAACTCATAAGCGTCTTATCGAAAAAGAGCTAGAGGGAT
     | | ||| ||| |   || |        |  ||   |  | | |   | |  || || | | |  |  |||  ||| |  |    |||  |  | || |||||||| || ||||| |||||||||||||||||||||||||| ||||||||||| |||||||| ||||| |||||||| || || |||||||| |||||||
-----taataat-cacttagtatgtaatgtttcttgtttgtatgcaatcttcatatgctcatccttctggctcaatatattaaaatggcatgtcatcaatatccagGTTATCAGCACTGCTAGAACATGCAATTGCATTTTGATTGTTCTTGATGCAATAAAGCCAATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGAT

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|163920656|gb|EH039949.1|EH039949
EST:     TCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG                         GTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCA
genomic: TCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAGgtaaaaaaaa ... ggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCA
EST: gi|16996121|gb|BM085493.1|BM085493
EST:     TCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG                         GTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCA
genomic: TCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAGgtaaaaaaaa ... ggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCA
EST: gi|7041848|gb|AW471742.1|AW471742
EST:     TCCCTGGAATTATCGATGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG                         GTTATTAGTACTGCA
genomic: TCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAGgtaaaaaaaa ... ggaaatgcagGTTATTAGTACTGCA
EST: gi|151412834|gb|EV282646.1|EV282646
EST:     TCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG                         GTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCA
genomic: TCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAGgtaaaaaaaa ... ggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCA
EST: gi|254315459|gb|GR825268.1|GR825268
EST:     TCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG                         GTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCA
genomic: TCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAGgtaaaaaaaa ... ggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCA
EST: gi|151406659|gb|EV276474.1|EV276474
EST:     TCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAG                         GTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCA
genomic: TCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAGgtaaaaaaaa ... ggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacaaacactgatacattttcgtaattcatttatttattgttttggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCAATTAAGCCAATAACTCATAAGCGTCTTATCGAAAAAGAGCTAGAGGGAT
       cactgat  putative branch site (score: 3)
                attttcgtaattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acctttcacaatgcacctttcattttccacacttcattcacacaccaacaaacactgatacattttcgtaattcatttatttattgttttggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCAATTAAGCCAATAACTCATAAGCGTCTTATCGAAAAAGAGCTAGAGGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
-cctttca
- - - - - -tgcacct
- - - - - - - - - - - - - ccacact
- - - - - - - - - - - - - - - - - - - -acacacc
- - - - - - - - - - - - - - - - - - - - - - - - caaacac