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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcctgctatcttcgtaaagtgtgttaattctttgtaatttaacggttgcaactcttagctcctaacattcttcatttcagGAGAAAGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGTGAAATATATCAAGATGCAGATGAGGATACAAGGAGGGCAATGAAAAAGT

Basic information

species Glycine max
transcript GLYMA16G29450.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 8
gtttgcctgctat-cttcgtaaagtgtgttaattctttgtaa------tttaacggttgcaactctt-agctcctaacattcttcatttc----agGAGAAAGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGTGAAATATATCAAGATGCAGATGAGGATACAAGGAGGGCAATGAAAAAGT
||| |  || |   | | ||  |  || | | | | |    |      || |||  | | || | || |  | | |  | | |  |||||    ||||||| || || |||||||| ||||||||||| |||||||||||||||||||| || ||    ||||| ||||| || |   |  | |||||||  || |
gttagtatgatgcacatggttcaacgtttcactgcctgtggacattccttgaactctggtaattattgaattgccatgactttgaatttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGTGACATCTACAGTGATGCTGATGAAGACATGCGACGAGCAATGATGAAAT

upper sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 8
gtttgcctgctatcttcgta---aagtgtgttaattct-ttgtaa---------tttaacggttgcaactcttagctcctaacat-tcttcatttcagGAGAAAGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGTGAAATATATCAAGATGCAGATGAGGATACAAGGAGGGCAATGAAAAAGT
|||||      ||| ||      |  ||| |  ||  | |||  |         |||| ||  |   | |      || | |  | | |     ||||||||| || ||||| |||||||| |||||||| ||||||||||| |||||||| || ||  | ||||| ||||| ||||   ||||||| ||||  ||||
gtttgatgaagatcctcacttatatatgtatcgatcttattgctagaacttgggtttatcgaatatgaatggggtttcatgatttgtgtctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT

upper sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------gtttgcctgctatcttcgtaaagtgtgtta----attctttgtaatttaacggttgcaactcttagctcctaacattcttcatttcagGAGAAAGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGTGAAATATATCAAGATGCAGATGAGGATACAAGGAGGGCAATGAAAAAGT
                           ||||  |   ||  | ||  |   |  ||    |  ||  | ||||| |   |||    ||  |     |     | |  ||||||||||||||| |||||||| ||||| ||||| ||  |||||||||||||||| || |||||| |||||||||| || || ||||| ||||| ||| |||| |
gtttgcctgcaatctagatcctgttactttggttttcattattgtttaacatcatatgagaacctgaggaattttat--ttgggggtca-actctttggtggtttgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAAT

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|5677947|gb|AI939077.1|AI939077
EST:     CAAAACAAACAAGAGACTGCGACAAGATTGAAGCTCAAGTCAAGACAGAG                         GAGACAGACTGAAA-GCTTGATGGCGATGCTGCGTTGAACAAACTGTTCCG
genomic: CAAAACAAACAAGAGACTGGGACAAGATTGAAGCTCAAGTCAAGAAAGAGgtttgcctgc ... ttcatttcagGAGAAAGAC-GAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCG
EST: gi|37994197|gb|CF805943.1|CF805943
EST:     CAAGATTGAAGCTCAAGTCAAGAAAGAG                         GAGAAAGACGAAAAGCTTGATGCCGATGCTGCGTTGAACAAATTTTTCCGT
genomic: CAAGATTGAAGCTCAAGTCAAGAAAGAGgtttgcctgc ... ttcatttcagGAGAAAGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGT
EST: gi|213593229|gb|DB973534.1|DB973534
EST:     CAAAACAAACAAGAGACTGGGACAAGATTGAAGCTCAAGTCAAGAAAGAG                         GAGAAAGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGT
genomic: CAAAACAAACAAGAGACTGGGACAAGATTGAAGCTCAAGTCAAGAAAGAGgtttgcctgc ... ttcatttcagGAGAAAGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattctttgtaatttaacggttgcaactcttagctcctaacattcttcatttcagGAGAAAGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGTGAAATATATCAAGATGCAGATGAGGATACAAGGAGGGCAATGAAAAAGT
                                  tcctaac  putative branch site (score: 1)
                                          ttcttcatttc  CT-rich tract
     tttgtaatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcctgctatcttcgtaaagtgtgttaattctttgtaatttaacggttgcaactcttagctcctaacattcttcatttcagGAGAAAGACGAAAAGCTTGATGGCGATGCTGCGTTGAACAAATTTTTCCGTGAAATATATCAAGATGCAGATGAGGATACAAGGAGGGCAATGAAAAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG