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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagctactccaaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC

Basic information

species Glycine max
transcript GLYMA04G06810.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 4
aagctactccaaattgaagctact-ccaggagaattttaca-attgacattttgaagattaataaatgctgtctcacaatttgttcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC
    ||   ||  |   || |||    |  ||   ||     |||  | |||  |  | | ||         ||||     ||||  | ||  ||| |  |||||||||| ||||| || |||||||||||||| || ||||| ||||| ||||||||||||||||||||||| ||| | ||  |||||||||| ||||| |
---gtatgtcagctcacagataccattatcaggccttcctgcatttccttttctaccactgatg--------ctca-----tgtttcttaacctttat--agGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC

upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g19650.1 (Oryza sativa), 3'ss of exon 4
aagctactc--caaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC
| ||   |   | | |||   |  |||          ||     ||    |   | |||  | | |  |||  |  |  |   || ||    ||  | | ||||||| || ||||||||| | || || ||||| ||  | ||||||||||||||||| || ||||| ||||| |||||||| || |||||||| || ||||
atgccgtttggccacttgtgccctctcttttcatccattttgggtgttcatcacaggatgtacata-actgaattcctctcccttttttttcgtcatgt-agGAGGAAGACAAGGCACGGCTAGTCCAAGAAACAGGGCTACAGCTAAAGCAGATCAACAACTGGTTCATCAACCAAAGGAAAAGAAACTGGCACAGTAACC

upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 4
aagctactccaaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC
    |||     |   |   | |        || ||||  |||    | |  |    |  |   |  || |   |||||  |||| ||     | ||||||| || || ||||| ||  |||||||||||||||| || || || ||||| ||||| |||||||| || || ||| | ||  | ||||||||||||||||
---gtacgtggcaccaacattccatttccgtaactttattattatggtatcaa----ttgtgggtcatgacgagcaattctttctaca---catattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC

upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
aagctactccaaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttcaat-gttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC
    ||    | | |   || ||      | ||||      |  || |||     || |      | |   |    ||    ||||   |  ||  | ||||| || || ||||||||  |||||||||||||||| ||||||||||||||||| || || ||||| ||||| ||| | ||  |||||||||| |||||||
---gtatgtgacactacggcgacat----ataattccctcgtcaactttt--gctatcagcttgggttcattgctgatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC

upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
aagctactccaaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttcaat-gttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC
           |  |||  |  |  ||    ||||      ||  | | |     || |      |||   | |  |     ||||   |   |  | ||||| || || |||||  |  |||||||||||||||| |||||||||||||| ||||| || ||||| || || ||| | ||| |||||||||| |||||||
---------gtacgtgacaccgcgtcaacttaattccctcgttagcttct--gctatcaggttcggctcattgatgagcaactctttgcttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC

upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------aagctactccaaattgaagctactccaggagaattttacaattgacattttgaa---gattaataaatgctgtctcacaatttgttcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC
                                          || |||||   |    |      |   ||  |  |      |  || |   |     |||  ||  | ||       |  || |  |  |    || || ||||||| || ||||| ||  ||||||||||||| ||  | || || |||||||||||||| ||||||||||| ||  | ||| |||||||||| | |||  
gtaagtgaacacattgatcctatcactcccagcaccattcctagttactcatgagcatattattacgttgaacacatggatcctatcactcccagcaccattcctatttactcatgagtatattatcgtggaccacttgtttagGAGGAAGACAAGGCTCGACTGGTGCAGGAAACAGGGCTACAACTGAAGCAGATCAATAACTGGTTTATCAACCAGCGTAAGCGGAACTGGCACAACAATT

upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24870 (Selaginella moellendorffii), 3'ss of exon 4
----------------------------------------------------------aagctactccaaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttca-atgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC
                                                          |   |  |  |  ||| | | ||  | | |  |    | ||        | |   ||   | | |  | | || |  | |  | |  |   ||| || ||||| || || ||||||||  | || ||||| || || ||| |||| ||||||||||| ||||||||||| || || |||||| | |||||||| ||||| |
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagattttggatccacaaccgaaagaaagaagaagcatggaatcgtttat-gcttatttttttttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC

upper sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ30264 (Selaginella moellendorffii), 3'ss of exon 4
----------------------------------------------------------aagctactccaaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC
                                                          |   |  |  |  ||| | | ||  | | |  |    | ||        | |   ||   ||  |  | |    |   |  ||  |    ||| || ||||| || || ||||||||  | || ||||| || || ||| |||| ||||||||||| ||||||||||| || || |||||| | |||||||| ||||| |
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagatgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttattttttcttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC

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|120494985|gb|EH223152.1|EH223152
EST:     CTGTCCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTACCCCACA                         GAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAG
genomic: CTGTCCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTACCCCACAgtaagaaccc ... gttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAG
EST: gi|193704072|gb|FK645236.1|FK645236
EST:     CATTCCAAGTGGCCTTACCCCCACA                         GAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCA
genomic: CATTCCAAGTGGCCTTA-CCCCACAgtaagaaccc ... gttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttgaagattaataaatgctgtctcacaatttgttcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC
                       gtctcac  putative branch site (score: 3)
                                            tgttttttc  putative PPT
     tgaagattaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagctactccaaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- -ctactcc
- - - ctccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgtc