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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcgtaacaacttttatttgatggaatggcgttgcttcaacacaagtgactgattttttatttgctatgatgtttaattgcctgtttcctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAGGATGGGTCCCAGGCAGCCCAAGGCTTGGTAGTTCGGTGAGGACGATTGA

Basic information

species Glycine max
transcript GLYMA20G22090.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G22090.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 9
ttttcgtaacaacttttatttgatggaatggcgttgcttcaacacaagtgactgattttttatttgctatgatgtttaattgcctgt---ttcctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAGGATGGGTCCCAGGCAGCCCAAGGCTTGGTAGTTCGGTGAG--GACGATTGA
   |  ||    ||||    | ||| | |  | ||    |    |   |     ||  ||  ||   | || ||||||||| |||     ||  | | ||||||| || ||||||||||| |||| ||||||||| |||||||| ||||  || ||||| || ||||||   |||||||||    | || | ||   |  | |  
---ttatatttgctttatcataatgtatttccattaacccctttcctttttgcaatggttacttatatttggtgtttaatttccttgatgtttttttctctagGGTAATATTGCAAATGTCATCAATACCATTCAAGCCAACAAGATAAGTGAAGATGGCTCTCAGGCAATGCAAGGCTTGACGATACGATAAGTTAATCACT--
















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|208032027|gb|GD827713.1|GD827713
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|27425907|gb|CA937427.1|CA937427
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|58021081|gb|CX707823.1|CX707823
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|193520423|gb|FK475488.1|FK475488
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGA
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGA
EST: gi|207830206|gb|GD804614.1|GD804614
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|20813000|gb|BQ297478.1|BQ297478
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|193610165|gb|FK565729.1|FK565729
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCA
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCA
EST: gi|6482099|gb|AW201370.1|AW201370
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|208131621|gb|GD926852.1|GD926852
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|15286594|gb|BI470485.1|BI470485
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCANGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|19453133|gb|BM954543.1|BM954543
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|31473744|gb|CD415772.1|CD415772
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|58017825|gb|CX704567.1|CX704567
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|31460889|gb|CD402917.1|CD402917
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|31561461|gb|CD487299.1|CD487299
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|13790301|gb|BG652892.1|BG652892
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|209729517|gb|BW651857.1|BW651857
EST:     CCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
genomic: CCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAG
EST: gi|192294162|gb|FG986251.1|FG986251
EST:     TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGG                         GGAAACATTGCAAATGTGATCAGTACCATTCACGCCAACAAAATAAC
genomic: TTGGTCAGCACCAATGGCAAGCACTGAGAACAAAGCTAGTGACATGGAGGgtaaagaatt ... ctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgactgattttttatttgctatgatgtttaattgcctgtttcctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAGGATGGGTCCCAGGCAGCCCAAGGCTTGGTAGTTCGGTGAGGACGATTGA
                                     cctgtttcctatttct  CT-rich tract
         attttttatttgctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcgtaacaacttttatttgatggaatggcgttgcttcaacacaagtgactgattttttatttgctatgatgtttaattgcctgtttcctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAGGATGGGTCCCAGGCAGCCCAAGGCTTGGTAGTTCGGTGAGGACGATTGA

- - - - - - - - - -ttgatgg
- - - - - - - - - - - - - - - - gttgctt
- - - - - - - - - - - - - - - - - - - -caacaca
- - - - - - - - - - - - - - - - - - - - - - - -gtgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcctgt