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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctgtcatagggaagctgactgatatgatatctattactccttgtacttggtggttgaaaaatccttttataacagactttgactttggtttatgcagGGTTTGGGGCCTTATTCCACAAGCATAAAAAAAGTCGAGAAGGAAATCAAAGACATGGCAAAAAAGGTCAATGATTTATGTG

Basic information

species Glycine max
transcript GLYMA19G45140.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 1
-tctctgtcatagggaagctgactgatatgatatctattactccttgtactt-ggtggttgaaaaatccttttataacagactttgactttggtttatgcagGGTTTGGGGCCTTATTCCACAAGCATAAAAAAAGTCGAGAAGGAAATCAAAGACATGGCAAAAAAGGTCAATGATTTATGTG
   |   |  | | |||  | | |  |  | | |   |  || |||  | || ||||| | |   ||   ||  |   |    ||||   |||||||||||||| ||||| ||||||||  ||   ||||| |||   ||||||||||| ||||| ||||| || |||||||| ||||||||||
aaattatttcttgtgaatttcatttttcagctgttattagcttcttagattttggtgggtcagttattagttcttctaaacagttgaa--tggtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAAGAAATGGCTAAGAAGGTCAACGATTTATGTG
















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|151411562|gb|EV281373.1|EV281373
EST:     AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTAT                         GGTTTGGGGCCTTATTCCACAAGCATNNNNNNNGTCGAGAAGGAAATCAAA
genomic: AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATgtatgtatgc ... gtttatgcagGGTTTGGGGCCTTATTCCACAAGCATAAAAAAAGTCGAGAAGGAAATCAAA
EST: gi|254338828|gb|GR847545.1|GR847545
EST:     AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTAT                         GGTTTGGGGCCTTATTCCACAAGCATNNNNNNNGTCGAGAAGGAAATCAAA
genomic: AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATgtatgtatgc ... gtttatgcagGGTTTGGGGCCTTATTCCACAAGCATAAAAAAAGTCGAGAAGGAAATCAAA
EST: gi|151410157|gb|EV279965.1|EV279965
EST:     AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTAT                         GGTTTGGGGCCTTATTCCACAAGCATNNNNNNNGTCGAGAAGGAAATCAAA
genomic: AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATgtatgtatgc ... gtttatgcagGGTTTGGGGCCTTATTCCACAAGCATAAAAAAAGTCGAGAAGGAAATCAAA
EST: gi|151406841|gb|EV276656.1|EV276656
EST:     AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTAT                         GGTTTGGGGCCTTATTCCACAAGCGTNNNNNNNGTCGAGAAGGAAATCAAA
genomic: AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATgtatgtatgc ... gtttatgcagGGTTTGGGGCCTTATTCCACAAGCATAAAAAAAGTCGAGAAGGAAATCAAA
EST: gi|254320308|gb|GR831116.1|GR831116
EST:     AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTAT                         GGTTTGGGGCCTTATTCCACAAGCATNNNNNNNGTCGAGAAGGAAATCAAA
genomic: AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATgtatgtatgc ... gtttatgcagGGTTTGGGGCCTTATTCCACAAGCATAAAAAAAGTCGAGAAGGAAATCAAA
EST: gi|208319181|gb|GE115876.1|GE115876
EST:     AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTAT                         GGTTTGGGGCCTTATTCCACAAGCAT
genomic: AGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATgtatgtatgc ... gtttatgcagGGTTTGGGGCCTTATTCCACAAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacttggtggttgaaaaatccttttataacagactttgactttggtttatgcagGGTTTGGGGCCTTATTCCACAAGCATAAAAAAAGTCGAGAAGGAAATCAAAGACATGGCAAAAAAGGTCAATGATTTATGTG
              aaaaatccttttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctgtcatagggaagctgactgatatgatatctattactccttgtacttggtggttgaaaaatccttttataacagactttgactttggtttatgcagGGTTTGGGGCCTTATTCCACAAGCATAAAAAAAGTCGAGAAGGAAATCAAAGACATGGCAAAAAAGGTCAATGATTTATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- tctgtca
- - - - - - - - gctgact
- - - - - - - - - - - - - - - - - - - -ctccttg
- - - - - - - - - - - - - - - - - - - - - - - - - tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gactttg