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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGATATCCTTATACTTGACACACATGCAGAAGTGTTTATTTGGATTGGTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAGgtaaacatgctaaacaatttatggcttttatctcctatattgccttctacttgatattcttgatgcttactcaaaaatttccctcag

Basic information

species Glycine max
transcript GLYMA10G21350.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G21350.2 (Glycine max), 5'ss of exon 17
lower sequence: GRMZM2G047310_T01 (Zea mays), 5'ss of exon 16
GGAGGATATCCTTATACTTGACACACATGCAGAAGTGTTTATTTGGATTGGTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAGgtaaacatgctaaacaatttatggcttttatctcctatattgccttctacttgatattcttgatgcttactcaaaaatttccctcag
 || || ||  |  |||||||||||||||  ||||| || |||||||||||||| | ||||||| | ||||| || |  || || ||||| ||||||||||||   |  || ||    | |     || |  |  |   || |  | | || | | ||||  |||| ||     |  |||||  |||
TGAAGACATGATGGTACTTGACACACATGGTGAAGTTTTCATTTGGATTGGTCAGTATGTGGAATCAAAAGAGAAACAGAAGGCATTTGACATTGGCCAGgtatcaa--ctgaagccctgaccttattcaagtagtcagttcctgtttgct-gttgttctgtatgcgtaac--gacttttccaccag

upper sequence: GLYMA10G21350.2 (Glycine max), 5'ss of exon 17
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 5'ss of exon 17
GGAGGATATCCTTATACTTGACACACATGCAGAAGTGTTTATTTGGATTGGTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAGgtaaacatgctaaacaatttatggcttttatctcctatattgccttctacttgatattcttgatgcttactcaaaaatttccctcag
 ||||||||| | |||||||| |||||||| ||||| ||| ||||| |||||||  |||| || ||||| |||||||  | |||||||||||| || ||||||       ||| ||  ||||| | |||     | ||||| |  |  | |  || |   | || | |  |  ||  | |    |||
TGAGGATATCTTGATACTTGATACACATGCTGAAGTTTTTGTTTGGGTTGGTCAGACTGTAGATCCCAAGGAAAAGCAGAGTGCTTTTGAAATCGGTCAGgtacttgc-ttaagcagcttatgcccttt-----caatattactcttcaat-aatgtatcttattcattatggaagctcttttgcag
















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|193410500|gb|FK379833.1|FK379833
EST:     GTCATTCTGTGGAACCCAA-GAAAAGCGAAATGCTTTTGAAATTGGCCAG                         AAATACATAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACAATAGTAC
genomic: GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAGgtaaacatgc ... tttccctcagAAATACATAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACA-T-GTAC
EST: gi|9565739|gb|BE475248.1|BE475248
EST:     GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAG                         AAATACATAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACATGTACCA
genomic: GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAGgtaaacatgc ... tttccctcagAAATACATAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACATGTACCA
EST: gi|24206274|gb|BU965527.1|BU965527
EST:     GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAG                         AAATACATAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACATGTACCA
genomic: GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAGgtaaacatgc ... tttccctcagAAATACATAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACATGTACCA
EST: gi|33390214|gb|CA853421.1|CA853421
EST:     GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAG                         AAATACATAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACATGTACCA
genomic: GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAGgtaaacatgc ... tttccctcagAAATACATAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACATGTACCA
EST: gi|13481166|gb|BG510509.1|BG510509
EST:     GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAG                         AAATACATAGATTTGGTTGCATCTCTGGAGGGGC
genomic: GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAGgtaaacatgc ... tttccctcagAAATACATAGATTTGGTTGCATCTCTGGAGGGGC
EST: gi|26048794|gb|CA785247.1|CA785247
EST:     GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAG                         AAATACCTAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACATGTACCA
genomic: GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAGgtaaacatgc ... tttccctcagAAATACATAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACATGTACCA
EST: gi|193475713|gb|FK439428.1|FK439428
EST:     GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAG                         AAATACATAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACATGTACCA
genomic: GTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAGgtaaacatgc ... tttccctcagAAATACATAGATTTGGTTGCATCTCTGGAGGGGCTATCTCCACATGTACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGATATCCTTATACTTGACACACATGCAGAAGTGTTTATTTGGATTGGTCATTCTGTGGAACCCAAAGAAAAGCGAAATGCTTTTGAAATTGGCCAGgtaaacatgctaaacaatttatggcttttatctcctatattgccttctacttgatattcttgatgcttactcaaaaatttccctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA