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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcttggttgagtccttgctatggaaggtttgccggtggcagtgattttgtgagttgtgataattgttttgtcttgcttgcagACAGATGAGGTGCTTGAGTTGTCGAAGCAAATCAAAGAGAAATTGAAAGAAGCTGATCAATATG

Basic information

species Glycine max
transcript GLYMA18G47910.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47910.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtcttggttgagtccttgctatggaaggtttgccggtggcagtgattttgtgagttgtgataattgttttgtc---ttgcttgcagACAGATGAGGTGCTTGAGTTGTCGAAGCAAATCAAAGAGAAATTGAAAGAAGCTGATCAATATG
    ||  |||||||||     ||  ||   |||          | |   | | |   || ||||   |  ||| |    |   |||||||||  |||||||||||||||||||||||| || || ||||| ||||| ||||||||||||| ||
----gtagtggttgagttt---ctcaggctagttctttaaccata-tatatctatatattttgatggataatttattgattcctttgcagACACCTGAGGTGCTTGAGTTGTCGAAGCAGATTAAGGAGAAGTTGAAGGAAGCTGATCAATTTG
















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|10847913|gb|BF071644.1|BF071644
EST:     ATGACGATGCGAAAGCTGCGATTGCGATTTCGGTCTCTGAAGTTACTCAA                         ACAGATGAGGTGCTTGAGTTGTCGAAGCAAATCAAAGAGAAATTGAAAGAA
genomic: ATGACGATGCGAAAGCTGCGATTGCGATTTCGGTCTCTGAAGTTACTCAAgtgagtcttg ... ttgcttgcagACAGATGAGGTGCTTGAGTTGTCGAAGCAAATCAAAGAGAAATTGAAAGAA
EST: gi|192296271|gb|FG989063.1|FG989063
EST:     ATGACGATGCGAAAGCTGCGATTGCGATTTCGGTCTCTGAAGTTACTCAA                         ACAGATGAGGTGCTTGAGTTGTCGAAGCAAATCAAAGAGAAATTGAAAGAA
genomic: ATGACGATGCGAAAGCTGCGATTGCGATTTCGGTCTCTGAAGTTACTCAAgtgagtcttg ... ttgcttgcagACAGATGAGGTGCTTGAGTTGTCGAAGCAAATCAAAGAGAAATTGAAAGAA
EST: gi|208271764|gb|GE068686.1|GE068686
EST:     ATGACGATGCGAAAGCTGCGATTGCGATTTCGGTCTCTGAAGTTACTCAA                         ACAGATGAGGTGCTTGAGTTGTCGAAGCAAAT
genomic: ATGACGATGCGAAAGCTGCGATTGCGATTTCGGTCTCTGAAGTTACTCAAgtgagtcttg ... ttgcttgcagACAGATGAGGTGCTTGAGTTGTCGAAGCAAAT
EST: gi|209725035|gb|BW659770.1|BW659770
EST:     ACGACGATGCGAAAGCTGCGATTGCGATTTCGGTCTCTGAAGTTACTCAA                         ACAGATGAGGTGCTTGAGTTGTCGAAGCAAATCAAAGAGAAATTGAAAGAA
genomic: ATGACGATGCGAAAGCTGCGATTGCGATTTCGGTCTCTGAAGTTACTCAAgtgagtcttg ... ttgcttgcagACAGATGAGGTGCTTGAGTTGTCGAAGCAAATCAAAGAGAAATTGAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgccggtggcagtgattttgtgagttgtgataattgttttgtcttgcttgcagACAGATGAGGTGCTTGAGTTGTCGAAGCAAATCAAAGAGAAATTGAAAGAAGCTGATCAATATG
                                      ttttgtctt  CT-rich tract
                               ataattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcttggttgagtccttgctatggaaggtttgccggtggcagtgattttgtgagttgtgataattgttttgtcttgcttgcagACAGATGAGGTGCTTGAGTTGTCGAAGCAAATCAAAGAGAAATTGAAAGAAGCTGATCAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT