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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGATGAATGTATTTCGGAAAAATTATGATCTTTTGTTGGGCATCTTCAATCCAGAGGGATGGCTGGAAATCACgtatcctaattctttgaagatttttcttcttcttttcttttattggtctaattttgaggtccaacccatatctactctttttgacgagcccaaatcatgtctttctttgttttctcatgctttttattattgatgaaatttgttgttgttcctaaactccattatgccatag

Basic information

species Glycine max
transcript GLYMA05G32170.1
intron # 5
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32170.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv04s0044g00530.t01 (Vitis vinifera), 5'ss of exon 6
TTGATGAATGTATTTCGGAAAAATTATGATCTTTTGTTGGGCATCTTCAATCCAGAGGGATGGCTGGAAATCACgtatcctaattctttgaagatttttcttcttcttttcttttattggtctaattttgaggtccaacccatatctactctttttgacgagcccaaatcatgtctttctttgtttt-ctcatgctttttattattgatgaaatttgttgttgttcctaaactccattatgccatag
||||||||||| ||   | |||| ||||||||| || ||||||||||||| |||||||| ||||| || ||||||||||||  |||| | |        |||      |  ||     |  |||  ||||||  ||  || |||   ||| ||| |             | ||| |||    |  |   || | |      || |  || | |      |||||||||  | ||||    | || ||
TTGATGAATGTGTTCAAGCAAAACTATGATCTTCTGCTGGGCATCTTCAACCCAGAGGGTTGGCTTGAGATCACgtatcct--ttctatca--------ctttgggagtaattgaggcgaccta--tttgagaccct-cctataaa-actgtttctttttttttttttccctgtattttaaagaatagttcctccaacaggttctgaatcagaacaa--gttgttccttgattccac--cgtcacag
















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|22932717|gb|BU549856.1|BU549856
EST:     CTTCAATCCAGAGGGATGGCTGGAAATCAC                         ATATGTTGATGATACCTTGAGAATAGGAAGGGACGACAAAAGCAATATCTT
genomic: CTTCAATCCAGAGGGATGGCTGGAAATCACgtatcctaat ... tatgccatagATATGTTGATGATACCTTGAGAATAGGAAGGGACGACAAAAGCAATATCTT
EST: gi|22928718|gb|BU545857.1|BU545857
EST:     TATGATCTTTTGTTGGGCATCTTCAATCCAGAGGGATGGCTGAAAATCAC                         ATATGTTGATGATACCTTGAGAATAGGAAGGGACGACAAAAGCAATATCTT
genomic: TATGATCTTTTGTTGGGCATCTTCAATCCAGAGGGATGGCTGGAAATCACgtatcctaat ... tatgccatagATATGTTGATGATACCTTGAGAATAGGAAGGGACGACAAAAGCAATATCTT
EST: gi|13478869|gb|BG508212.1|BG508212
EST:     CAATCCAGAGGGATGGCTGGAAATCAC                         ATATGTTGATGATACCTTGAGAATAGGAAGGGACGACAAAAGCAATATCTT
genomic: CAATCCAGAGGGATGGCTGGAAATCACgtatcctaat ... tatgccatagATATGTTGATGATACCTTGAGAATAGGAAGGGACGACAAAAGCAATATCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGATGAATGTATTTCGGAAAAATTATGATCTTTTGTTGGGCATCTTCAATCCAGAGGGATGGCTGGAAATCACgtatcctaattctttgaagatttttcttcttcttttcttttattggtctaattttgaggtccaacccatatctactctttttgacgagcccaaatcatgtctttctttgttttctcatgctttttattattgatgaaatttgttgttgttcctaaactccattatgccatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA