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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgatgtatgtgatatataatataattcgttttttgataaaattatgtataaaataatatatattctcataaatggattcaaacttttgtgcggatgcagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCAT

Basic information

species Glycine max
transcript GLYMA05G08040.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 17
ctgatgtatgtgatatataatata-attcgttttttgataaaattatgtataaaataatatatattctcataaatggattcaaacttttgtgcggatgcagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCAT
         ||  | | || | || | || |  | | ||     | |    ||| |    |||||  ||  |    | | |||| ||           |||||||| || || ||||| ||  | || || || |||||||| || ||  | |||||||||||||||||| | ||||| || |||||||||||| | ||||
---------gtagtgtttagtctagaatcatcctattattttcatttcctgaaattgggctatatgttctcatgctg-tgcaaattt-----------cagGTTGGAGGTATTTATGTGAGACTCTTCCTAAAGGATCCCAAGTTTCCATTGAGAAACCCTAAAAGGTTCCTAGAAGGGCTGCTAGATCAGTATGTCTCAT

upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G049288_T01 (Zea mays), 3'ss of exon 17
ctgatgtatgtgatatataatataattcgttttttgataaaattatgtataaaataata-tatattctcataaatggattcaaacttttgtgcggatg-cagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCAT
         ||  | | || |  |   | ||||||| |        || |||||||||  | ||   |     | |   ||    |  ||| |  ||  ||||||||||| || ||||| ||  | ||||| || |||||||| || || || |||||||||||||| ||| | ||||| || |||||||||||| | || |
---------gtagtttctattccagaac-ttttttgtt--------gtgtaaaataattctgtaactttgcttaagatgtcggtatgctgtccaaatttcagGTTGGTGGAATTTATGTAAGACTTTTTCTTAAGGATCCCAAGTTTCCACTGAGAAACCCTAAAAGATTCCTTGAAGGGCTCCTAGATCAGTATGTCTCCT

upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 11
ctgatgtatgtgatatataatataattcgttttttgataaaattatgtataaaataata-tatattctcataaatggattcaaacttttgtgcggatg-cagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCAT
         ||    | || |  |   | |||||           || |||| |||||  | ||   | |   | |   |||   |  ||| |  ||  ||||||||||| || ||||||||  | ||||| || || |||||||| || || |||||||||||||| ||| | ||||| || |||||||| ||| | || |
---------gtagcttctattccagaacttttttct---------tgcataatataattctgtaactttagttaagatgtcagtatgctgtccaaatttcagGTTGGTGGAATTTATGTTAGACTTTTTCTTAAGGACCCCAAATTTCCACTGAGAAACCCTAAAAGATTCCTTGAAGGGCTCCTAGATCAATATGTCTCCT

upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 17
ctgatgtatgtgatatataatataattcgttttttgataaaattatgtataaaata-atatatattctcataaatggatt-caaacttttgtgcggatgcagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCAT
                    |||     ||| | |  |    || |   | |||||  ||  | | ||  | | |||||| |||| |||  ||   ||||||||||| || |||||||||||| | ||  ||||||||||||| || ||||||||||| || || |||||||||||||| || ||||| |||||| | ||||
-------------------gtatctcctgttctattctgtcctttttattcaaatatgtacctgtactgttgagtggatttcaaattttcatggtcatgcagGTTGGAGGAATCTATGTTAGGCTTTTCTTGAAAGATCCCAAGTTTCCTCTTAGAAATCCAAAGAGGTTCTTGGAAGGACTGCTAGACCAGTATCTTTCAT

upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S107_71V6.1 (Physcomitrella patens), 3'ss of exon 20
--------------------------------------------------------------ctgat--gtatgtgatatataatataattcgtttt-ttgataaaattatgtataaaataatatatattctcataaatggattcaaacttttgtgcggatgcagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCAT
                                                               |  |  || |||||| ||  | | ||||| | |   |  |    |  |  |||   | |  | |  |  ||||     | ||| |   || |  |    |||||||||||  | |||||| | ||||| |||||||||||||||||||||||| |||| || ||  ||||||| || ||| |||| || || ||| |  || 
gtaatttttcatatggttgttatttttctcttgtcttaaaattttaagatggttttatttttgtagttcgtctgtgatgtagtagaaaattcctctggcttcttcggtggttgatatcctcacttcttgttgcatactgtcactcataagcttttttgacctcagGTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTTCGAAATCCGAAGCGGTTCTTAGAGGGTTTACTTGACCAATATGTCACAG

upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S60_221V6.1 (Physcomitrella patens), 3'ss of exon 18
---------------------------------------------------------------------ctgatgtatgtgatatataat-----ataattcgttttttgataaaattatgtataaaataatatatattctcataaatggattcaaacttttgtgcggatg-----cagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCAT
                                                                      | ||||    ||  ||   |      |   | | |  |||||| |||| | | |    |  |||   | |   | | | | ||||   |||||| |   |      |||||||||||  | |||||  | ||||| ||||||||||| |||||||||||||||||||||||  ||||||| |||||  | ||||| || ||| || || 
gtctgcacatttttttatcgtgcttttctgtatttaagaatgccaaagttgacatttcgtaaactgtctttaatgtcgtagacttactctcgtgggttcattggtgattgatataattttcttttttttcgtatcc-tccatgttatttgcttcattgttttgtactttttatcctcagGTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTTAGAAACCCTAAGCGGTTCTTAGAAGGGTTGCTAGACCAATATGTGACAG

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|192298185|gb|FG992035.1|FG992035
EST:     ATTTGCCTGAGCAGGCATCTGGCCAGCAGGAAATGAGAGATGAGCCACAG                         GTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTT
genomic: ATTTGCCTGAGCAGGCATCTGGCCAGCAGGAAATGAGAGATGAGCCACAGgtatcacctg ... gcggatgcagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTT
EST: gi|192294376|gb|FG987305.1|FG987305
EST:     ATTTGCCTGAGCAGGCATCTGGCCAGCAGGAAATGAGAGATGAGCCACAG                         GTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAAT
genomic: ATTTGCCTGAGCAGGCATCTGGCCAGCAGGAAATGAGAGATGAGCCACAGgtatcacctg ... gcggatgcagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAAT
EST: gi|7590167|gb|AW705926.1|AW705926
EST:     ATTTGNCTGAGCAGGCATCTGGCCAGCATGAAATGAGAGATGAGCCACAG                         GTTGGTGGCATCTATGTTAG-TTGTTTC
genomic: ATTTGCCTGAGCAGGCATCTGGCCAGCAGGAAATGAGAGATGAGCCACAGgtatcacctg ... gcggatgcagGTTGGTGGCATCTATGTTAGGTTGTTTC
EST: gi|9565715|gb|BE475224.1|BE475224
EST:     ATTTGCCTGAGCAGGCATCTGGCCAGCAGGAAATGAGAGATGAGCCACAG                         GTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTT
genomic: ATTTGCCTGAGCAGGCATCTGGCCAGCAGGAAATGAGAGATGAGCCACAGgtatcacctg ... gcggatgcagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtataaaataatatatattctcataaatggattcaaacttttgtgcggatgcagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCAT
     aaaataatatatattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgatgtatgtgatatataatataattcgttttttgataaaattatgtataaaataatatatattctcataaatggattcaaacttttgtgcggatgcagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaact