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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagcattataacattaaataactgaccatttcccactactcctgaggaagaagggggcagcagatacaggtatactaacattttcttttcttttattagGTACCTTTATGATCTATTGACTAAAGGAAGTGTTGTGAGGAAGAAGATTCCAGTGCTTATTCTCTGCAACAAAACAGACAAAGTCACTGCTCATACTAAA

Basic information

species Glycine max
transcript GLYMA01G03540.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03540.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0127g00270.t01 (Vitis vinifera), 3'ss of exon 5
ttagcatt-ataacattaaataactgaccatttcccactactcctgaggaagaagggggcagcagatacaggtatactaacattttcttttcttttattagGTACCTTTATGATCTATTGACTAAAGGAAGTGTTGTGAGGAAGAAGATTCCAGTGCTTATTCTCTGCAACAAAACAGACAAAGTCACTGCTCATACTAAA
   | ||| |  |     | ||  ||    |  | ||    | |  |  || | |       || |      | || | |    |  |||   |  |  |||||||| |||||| | ||||||||    |||||||| | |||||| |||||||| || || |||||||||||||| |||||||| ||||||||||| || 
---gtatttactagccacagtatatggttttcacacatagatac--ataaatatgctactgccataatggattctaatcattggtgttttatatgcaaaagGTACCTGTATGATATTTTGACTAAGTCGAGTGTTGTCAAGAAGAAAATTCCAGTTCTCATCCTCTGCAACAAAACTGACAAAGTAACTGCTCATACCAAG
















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|17021044|gb|BM092078.1|BM092078
EST:     TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGA                         GTACCTTTATGATCTATTGACTAAAGGGAGTGTTGTGAGGAAGAAGATTCC
genomic: TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGAgtaattcctt ... cttttattagGTACCTTTATGATCTATTGACTAAAGGAAGTGTTGTGAGGAAGAAGATTCC
EST: gi|7925655|gb|AW831681.1|AW831681
EST:     TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGA                         GGACCTTTATGATCTATTG
genomic: TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGAgtaattcctt ... cttttattagGTACCTTTATGATCTATTG
EST: gi|9258120|gb|BE346267.1|BE346267
EST:     TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCGTCAGA                         GTACCTATATGATCTATTGACT
genomic: TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGAgtaattcctt ... cttttattagGTACCTTTATGATCTATTGACT
EST: gi|192319496|gb|FK005936.1|FK005936
EST:     TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGA                         GTACCTTTATGATCTATTGACTAAAGGAAGAGTTGTGAGGAAGAAGATTCC
genomic: TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGAgtaattcctt ... cttttattagGTACCTTTATGATCTATTGACTAAAGGAAGTGTTGTGAGGAAGAAGATTCC
EST: gi|213597292|gb|DB962082.1|DB962082
EST:     TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGA                         GTACCTTTATGATCTATTGACTAAA
genomic: TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGAgtaattcctt ... cttttattagGTACCTTTATGATCTATTGACTAAA
EST: gi|15814018|gb|BI786293.1|BI786293
EST:     TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGA                         GTACCTTTATGATCTATTGACTAAAGGAAGTGTTGTGAGGAAGAAGATTCC
genomic: TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGAgtaattcctt ... cttttattagGTACCTTTATGATCTATTGACTAAAGGAAGTGTTGTGAGGAAGAAGATTCC
EST: gi|192319497|gb|FK005937.1|FK005937
EST:     TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGA                         GTACCTTTATGATCTATTGACTAAAGGAAGAGTTGTGAGGAAGAAGATTCC
genomic: TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGAgtaattcctt ... cttttattagGTACCTTTATGATCTATTGACTAAAGGAAGTGTTGTGAGGAAGAAGATTCC
EST: gi|207713636|gb|GD695311.1|GD695311
EST:     TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGA                         GTACCTTTATGATCTATTGACTAAAGGAAGTGTTGTGAGGAAGAAGATTCC
genomic: TTTGTGGTAGATGCTTTGGACTTTTTACCAAACTGCCGTGCTGCTTCAGAgtaattcctt ... cttttattagGTACCTTTATGATCTATTGACTAAAGGAAGTGTTGTGAGGAAGAAGATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggaagaagggggcagcagatacaggtatactaacattttcttttcttttattagGTACCTTTATGATCTATTGACTAAAGGAAGTGTTGTGAGGAAGAAGATTCCAGTGCTTATTCTCTGCAACAAAACAGACAAAGTCACTGCTCATACTAAA
                            tactaac  putative branch site (score: 0)
                                  cattttcttttctttt  CT-rich tract
                          tatactaacattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagcattataacattaaataactgaccatttcccactactcctgaggaagaagggggcagcagatacaggtatactaacattttcttttcttttattagGTACCTTTATGATCTATTGACTAAAGGAAGTGTTGTGAGGAAGAAGATTCCAGTGCTTATTCTCTGCAACAAAACAGACAAAGTCACTGCTCATACTAAA

- - - - - - - - - - - ctgacca
- - - - - - - - - - - - - - - ttcccac
- - - - - - - - - - - - - - - - - - - -ctcctga
- - - - - - - - - - - - - - - - - - - - - - - - - gaagggg