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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagggtagctttatttgtttcattttttcatcttatgcattggcaagtttatgattaaatcaatttggatctatatataccaacattttggtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATATCAGGCATGGCTTGGTTACTACAATTCCAACAAGAAAGTAGGGCGTGACA

Basic information

species Glycine max
transcript GLYMA16G02880.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G041732_T01 (Zea mays), 3'ss of exon 9
aagggtagctttatttgtttcattttttcatcttatgcattggcaagtttatgattaaatcaatttggatctatatatacca-acattttg---gtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATATCAGGCATGGCTTGGTTACTACAATTCCAACAAGAAAGTAGGGCGTGACA
||   | |   | |   |   | ||  | |   |||| |     |  |  | |         | ||| ||     || |      ||||||     ||    |||| || || |||||  | ||||||||| | ||  | || ||| | || |||||||| |||||||||||||||||||| || |||    | ||||| ||||
aaatat-gtactgtacctacaacttcgtaagtctatgtagaacaatatccaagtc---gctgacttgcattatgctacattgtgtattttgtaatcgtgagtagGTCGATAAGGCTCTTGCACATGTGGAGGTTAAAGACAAGGAATCCGCTTATCAGGCGTGGCTTGGTTACTACAATTCAAATAAGGTCATTGGGCGCGACA

upper sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv15s0046g01010.t01 (Vitis vinifera), 3'ss of exon 10
--------aagggtagctttatttgtttcattttttcatcttatgcattggcaagtttatgattaaatcaatttggatctatatataccaacattttggtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATATCAGGCATGGCTTGGTTACTACAATTCCAACAAGAAAGTAGGGCGTGACA
        ||    |||||||| |  |  |       ||  |  | ||||  || |     |  | ||  || ||  | |||  | ||   | | |   ||||  ||||||||    || || ||||| |||||||||||||  |||||||||||||| || ||||||||||| ||||||||||| || ||||| || || || ||||
ggcatggaaaacacagctttatctcgtaaagca---aattctcagtattg--aaatgacatacaagattgatctgtgt-tatg-acacttgcgtgtatatgtt-gcagGTGGAGCGGGCACTGTCCCAAGTGGAGATGAAGAGCAAAGAAGCAGCATACCAAGCATGGCTTGGATACTACAATTCGAATAAGAAGGTGGGTCGGGACA
















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|193423761|gb|FK388532.1|FK388532
EST:     TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAG                         GTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
genomic: TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAGgtatttactt ... gtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
EST: gi|23730130|gb|BU763176.1|BU763176
EST:     GCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAG                         GTGGAAAAAGCTCTATCCCATGTGGAGATGAAGCATAAAGAAGCAGCATAT
genomic: GCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAGgtatttactt ... gtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
EST: gi|193644045|gb|FK588698.1|FK588698
EST:     TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAG                         GTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
genomic: TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAGgtatttactt ... gtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
EST: gi|120494906|gb|EH223073.1|EH223073
EST:     TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAG                         GTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
genomic: TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAGgtatttactt ... gtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
EST: gi|22931348|gb|BU548487.1|BU548487
EST:     TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAG                         GTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
genomic: TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAGgtatttactt ... gtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
EST: gi|208304421|gb|GE103914.1|GE103914
EST:     TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAG                         GTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
genomic: TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAGgtatttactt ... gtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
EST: gi|120494642|gb|EH222809.1|EH222809
EST:     TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAG                         GTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
genomic: TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAGgtatttactt ... gtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT
EST: gi|31465934|gb|CD407962.1|CD407962
EST:     TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAG                         GTGGAAAAAGCTCTATCCCATGTGGAGATGAAGCATAAAGAAGCAGCATAT
genomic: TTGAGAAAGCTCCCGTGTTACCTTCAGTTGATCCTGATACTAAGAAAAAGgtatttactt ... gtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttatgattaaatcaatttggatctatatataccaacattttggtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATATCAGGCATGGCTTGGTTACTACAATTCCAACAAGAAAGTAGGGCGTGACA
     atgattaaatcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagggtagctttatttgtttcattttttcatcttatgcattggcaagtttatgattaaatcaatttggatctatatataccaacattttggtgtttacagGTGGAAAAAGCTCTATCCCATGTGGAGATGAAGAATAAAGAAGCAGCATATCAGGCATGGCTTGGTTACTACAATTCCAACAAGAAAGTAGGGCGTGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - -tatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaacat