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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcccctttactaaaagcaacttaaatattcgttttcacaggtagtgatattattgcgctttagttgatcttaaaatgatttcctctgttggtgtccagGGTCAATTGTTCCGACTGATGCAACAACTAGAGAGTACTACTCCACATTTTATTCGCTGCATTAAACCGAATAATCTCCAATCACCTGAATCATATGAGC

Basic information

species Glycine max
transcript GLYMA09G42180.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 17
tttcccctttactaaaagcaacttaaatattcgttttcacaggtagtgatattattgcgctttagttgatcttaaaatgatttcctctgttggtgtccagGGTCAATTGTTCCGACTGATGCAACAACTAGAGAGTACTACTCCACATTTTATTCGCTGCATTAAACCGAATAATCTCCAATCACCTGAATCATATGAGC
 | |   |||   |    ||    | | |  |  | |   || |  ||||   ||        |||| |  | | || |  | | | | |||     ||||||||| |||||| ||| ||||||  ||| || ||||| || ||||| |||||||| ||||||||||| |||||| | |||   |||| |   ||||| |
gtgcagattttgcactcccag---agagagccactctgctagatcttgattgaatcagaac--agtttaattgacaacgtgtgcattttttg-----cagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACACCACACTTTATTCGTTGCATTAAACCAAATAATTTACAACTTCCTGCAATTTATGAAC

upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 17
tttcccctttactaaaagcaacttaaatattcgttttcacaggtagtgatattattgcgctttagttgatcttaaaatgatttcctctgttggtgtccagGGTCAATTGTTCCGACTGATGCAACAACTAGAGAGTACTACTCCACATTTTATTCGCTGCATTAAACCGAATAATCTCCAATCACCTGAATCATATGAGC
 | |   |||   |    ||    ||| |   ||| |   || |  |||| | ||        |||| |  | | ||  || | |  | ||    | ||||||||| |||||| ||| ||||||  ||| || ||||| || ||||| |||||||| ||||||||||| || ||| | |||   |||| |   ||||| |
gtgcagattttgcactcccag---aaagagctgttctgctagatcttgatgtaatcagaac--agttcaattgacaac-atgtgcaatttt----ttcagGGTCAACTGTTCCAACTTATGCAAAGACTGGAAAGTACAACGCCACACTTTATTCGTTGCATTAAACCAAACAATTTACAACTTCCTGCAATTTATGAAC
















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|208263892|gb|GE065300.1|GE065300
EST:     AGTCAGGTGGGGCAGATTCCCAAAAGCTAAGTGTTGCAACAAAATTCAAG                         GGTCAATTGTTCCGACTGATGCAACAACTAGAGAGTACTACTCCACATTTT
genomic: AGTCAGGTGGGGCAGATTCCCAAAAGCTAAGTGTTGCAACAAAATTCAAGgtacgctagc ... tggtgtccagGGTCAATTGTTCCGACTGATGCAACAACTAGAGAGTACTACTCCACATTTT
EST: gi|26056190|gb|CA799104.1|CA799104
EST:     CAAAAGCTAAGTGTTGCAACAAAATTCAAG                         GGTCAATTGTTCCGACTGATGCAACAACTAGAGAGTACTACTCCACATTTT
genomic: CAAAAGCTAAGTGTTGCAACAAAATTCAAGgtacgctagc ... tggtgtccagGGTCAATTGTTCCGACTGATGCAACAACTAGAGAGTACTACTCCACATTTT
EST: gi|6228015|gb|AW156543.1|AW156543
EST:     AGTCAAGTGGGGCAGATTCCCAAAAGCTA-GTGTTGCA-CAAAATTCAAG                         GGTCA-TTGTTCCGACTGATGCAACAACTA-AGAGTACTACTC-ACATTT-
genomic: AGTCAGGTGGGGCAGATTCCCAAAAGCTAAGTGTTGCAACAAAATTCAAGgtacgctagc ... tggtgtccagGGTCAATTGTTCCGACTGATGCAACAACTAGAGAGTACTACTCCACATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatattattgcgctttagttgatcttaaaatgatttcctctgttggtgtccagGGTCAATTGTTCCGACTGATGCAACAACTAGAGAGTACTACTCCACATTTTATTCGCTGCATTAAACCGAATAATCTCCAATCACCTGAATCATATGAGC
                  agttgat  putative branch site (score: 5)
                                   tttcctctgtt  putative PPT
                       atcttaaaatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcccctttactaaaagcaacttaaatattcgttttcacaggtagtgatattattgcgctttagttgatcttaaaatgatttcctctgttggtgtccagGGTCAATTGTTCCGACTGATGCAACAACTAGAGAGTACTACTCCACATTTTATTCGCTGCATTAAACCGAATAATCTCCAATCACCTGAATCATATGAGC

tttcccc
- - - - - - -aaaagcaa
- - - - - - - - - - - - - - - - - - - - -ggtagtg