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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGACTCCGATTTGTACCGGAAGCTTGTTATTGCTTCCGCTTGGAGGAAACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTGgtatagtgacaattaattacaattctcttaacttggttttgtggatttgttttttgttcagctgaaaattttgtgtttgtgtgaattgcttgtag

Basic information

species Glycine max
transcript GLYMA20G28440.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28440.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv05s0020g03470.t01 (Vitis vinifera), 5'ss of exon 1
GATGACTCCGATTTGTACCGGAAGCTTGTTATTGCTTCCGCTTGGAGGAAACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTGgtatagtgacaattaattacaattctcttaacttggttttgtggattt-gttttttgttcagctgaaaa--ttttgtgtttgtgtgaattgcttgtag--------
|| ||    ||||||||||||||||||||| |||  || || ||| |||| |||||||| ||||| ||  |||||||||| || | | |  ||||| | |||||  |     |  ||     || || |   || ||| | || |||| |||| | ||  |  | ||||    |  | |||     || |   ||           
GAAGATGTTGATTTGTACCGGAAGCTTGTTGTTGGGTCTGCGTGGCGGAAGCAGATGCCTAAGCTTGCTGTTTCGCTTGGGCTTGGTGATAAAATGGCCGgtatttt-----tccatcctgtttgtcctg-tttagttatatgcattttgtttctcgtcgaaataaaaagacataatttttccccaaactaagtggctgagctgcg
















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|254317673|gb|GR826657.1|GR826657
EST:     ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTG                         ATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
genomic: ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTGgtatagtgac ... ttgcttgtagATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
EST: gi|208236854|gb|GE029752.1|GE029752
EST:     TCAGCAAATGCCTG                         ATATGATTGAAGAGTTGATCA--AAAGGGCAGCAGCTTGATGCGGTTCACT
genomic: TCAGCAAATGCCTGgtatagtgac ... ttgcttgtagATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
EST: gi|254315365|gb|GR825174.1|GR825174
EST:     ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAA-TGCCTG                         ATATGATTGAAGAGTTGATCAGCA
genomic: ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTGgtatagtgac ... ttgcttgtagATATGATTGAAGAGTTGATCAGCA
EST: gi|254320461|gb|GR826910.1|GR826910
EST:     CGCTCAGCAAATGCCTG                         ATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
genomic: CGCTCAGCAAATGCCTGgtatagtgac ... ttgcttgtagATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
EST: gi|23733670|gb|BU765040.1|BU765040
EST:     ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTG                         ATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
genomic: ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTGgtatagtgac ... ttgcttgtagATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
EST: gi|298190258|gb|HO032379.1|HO032379
EST:     ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTG                         ATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
genomic: ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTGgtatagtgac ... ttgcttgtagATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
EST: gi|5058390|gb|AI736922.1|AI736922
EST:     ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTG                         ATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
genomic: ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTGgtatagtgac ... ttgcttgtagATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
EST: gi|254343680|gb|GR857436.1|GR857436
EST:     ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTG                         ATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT
genomic: ACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTGgtatagtgac ... ttgcttgtagATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGACTCCGATTTGTACCGGAAGCTTGTTATTGCTTCCGCTTGGAGGAAACAGATGCCGAAGCTCGCGCTTTCGCTTGGTCTCGCTCAGCAAATGCCTGgtatagtgacaattaattacaattctcttaacttggttttgtggatttgttttttgttcagctgaaaattttgtgtttgtgtgaattgcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG