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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttccttgatctgcatctattctagaatatttctttcattcttgcattttttacattttcttgcatatctccagctgattattattgcaatgtatgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGCATGAGAATAAGAAACAAGTTGGAGAACCTATAATAAG

Basic information

species Glycine max
transcript GLYMA04G07120.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G07120.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g10720.1 (Oryza sativa), 3'ss of exon 2
ttttccttgatctgcatctattctagaatatttctttcattcttgcattttttacattttc--ttgcatatctcca-gctgattattattgcaatgta--tgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGCATGAGAATAAGA---AACAAGTTGGAGAACCTATAATAAG
         | ||| | |||   ||  |  || | ||  | |   |  |   ||||| ||   ||   |   |  | | |||||||| |     |  |   | ||| ||||| || ||||||||||  || | ||||||||||||||||||||||||  |   | ||    |||||  | |||| || | ||||||
-----accaaactggaactaggttattacgttacattattacgaactatacgtacatgttaggttaagttcttttatgttgattattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG

upper sequence: GLYMA04G07120.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G097995_T02 (Zea mays), 3'ss of exon 2
ttttccttgatctgcatctattctagaatatttctttcattcttgcattttttacattttcttgcatatctccagctgattat--tattgcaatgtatgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGCATGAGAATAAGA---AACAAGTTGGAGAACCTATAATAAG
| |  | || |  |  |    | ||| |  |        || || ||||| ||    ||  ||| | ||||       |||    || |||    | | |||||||| | |||||||||||||  |||| |||||||||||||| || ||  |   |   ||      ||||   | ||||||| |   | ||
tgtagcatgctaagtgtgccat-tagtaagtggtgaatgttttt-catttattctcgttctttgtacatcttatttgaatttccatactgcctatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG
















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|298186285|gb|HO036918.1|HO036918
EST:     TCAAAGTAGTGCTGACATTCAGATTGATTCTTCTGAATATGTCAATCATG                         GTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGC
genomic: TCAAAGTAGTGCTGACATTCAGATTGATTCTTCTGAATATGTCAATCATGgcaagtattc ... atgtatgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGC
EST: gi|151409723|gb|EV279531.1|EV279531
EST:     TCAAAGTAGTGCTGACATTCAGATTGATTCTTCTGAATATGTCAATCATG                         GTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGC
genomic: TCAAAGTAGTGCTGACATTCAGATTGATTCTTCTGAATATGTCAATCATGgcaagtattc ... atgtatgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGC
EST: gi|58020771|gb|CX707513.1|CX707513
EST:     TCAAAGTAGTGCTGACATTCAGATTGATTCTTCTGAATATGTCAATCATG                         GTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGC
genomic: TCAAAGTAGTGCTGACATTCAGATTGATTCTTCTGAATATGTCAATCATGgcaagtattc ... atgtatgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGC
EST: gi|192332868|gb|FK024965.1|FK024965
EST:     TCAAAGTAGTGCTGACATTCAGATTGATTCTTCTGAATATGTCAATCATG                         GTCTTCTTCTCTGGAACCAGATGAGGCGACAGTGGGTTGGAAACAGAAGGC
genomic: TCAAAGTAGTGCTGACATTCAGATTGATTCTTCTGAATATGTCAATCATGgcaagtattc ... atgtatgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGC
EST: gi|298185514|gb|HO030727.1|HO030727
EST:     TCAAAGTAGTGCTGACATTCAGATTGATTCTTCTGAATATGTCAATCATG                         GTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACA
genomic: TCAAAGTAGTGCTGACATTCAGATTGATTCTTCTGAATATGTCAATCATGgcaagtattc ... atgtatgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttttacattttcttgcatatctccagctgattattattgcaatgtatgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGCATGAGAATAAGAAACAAGTTGGAGAACCTATAATAAG
                            agctgat  putative branch site (score: 4)
                                 attattattgcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttccttgatctgcatctattctagaatatttctttcattcttgcattttttacattttcttgcatatctccagctgattattattgcaatgtatgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGCATGAGAATAAGAAACAAGTTGGAGAACCTATAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA