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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgccggtcattcatgattaaattgatgataacattagttgaaacttttggcagttgataacatttttaaactcttgttttttttgtgaatgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA

Basic information

species Glycine max
transcript GLYMA12G30520.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 25
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 25
---------------ctgccggtcattcatgattaaattgatgataacattagttgaaacttttggcagttgataacatttttaaactcttgttttttttgtgaatgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA
                |  |  |   |  |  |   | |    |   || |   | ||| || |      | |||  | |            |||  || ||    ||| | |||| ||||||||||||||| ||||| ||||||||||| || ||| |||| || |  || || || || || || ||||||||
gtgagatttcaccaagtttcacttcctggttttggcacttgccactccaatttctaaaatttcttaagacttatagtaatgacgtgtgacattttccttggtttgcgattttcagGCAAGAATTGAAACAGACCCAGCGGACAGAACCCAACTACGATTGACAGTAGGCTCGGGAGATCCTACCCTTACATTTGA

upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 25
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 25
---------------------------------------ctgccggtcattca-tgattaaa-----ttgatgataacattagttgaaacttttggcagttgataacatttttaaactcttgttttttttgtga--------atgatgtgc-------agGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA
                                        ||||| || | || |   ||||     ||||   | | | || |       |   ||| |    ||  || | |||  | ||| | || |||||         || | |||       ||| |||||| |||||||| ||||| |||||||||||  |||||||||| || |   | || || || || || ||||||||
gtgagatcataaccaagttttacttcctggttttggcacttgccgctcttccaattcctaaaatttcttgagacttatagtaataacgtgatgctgcactcccaaaagttctcaaaagcctgtctgttgtgtgacattgtccgtggtttgctattgtcagGCAAGAATAGAAACAGACCCAGCGGACAGAACCCAATTGCGAATGACAGTAGGCACGGGAGATCCTACCCTTACATTTGA

upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 25
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 25
-ctgccggtcattcatgattaaattgatgata-acattagttgaaacttttggcagttgataacatttttaaactcttgttttttttgtgaatgatg-tgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA
 ||      | || |   | |||| ||||| | |   |   | | ||| | | |  |    || | |   |     |||  |||||| |  |||||| | ||| | ||||||||||||||||| ||||||||||| || || || ||||| ||| | ||||||||||| ||||||||||| ||
cctagtaaac-ttgaacctcaaatggatgaaacaagatgcatcatactgtagactttgaggaataatgccatctaattgccttttttat--atgatggtccagATGAGAATTGAAACAGATCCGGCAGACAGAACACAACTACGGATGACAGTTTCCTCAGGGGACCCTACACTAACATTCGA

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|192307606|gb|FG999645.1|FG999645
EST:     TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTA                         GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
genomic: TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTAgtaagtacat ... tgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
EST: gi|192307607|gb|FG999646.1|FG999646
EST:     TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTA                         GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
genomic: TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTAgtaagtacat ... tgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
EST: gi|21286017|gb|BQ473888.1|BQ473888
EST:     TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTA                         GTAAGAATTGAAACAGATCCAGCAGATATTAACCCAGCTGCGAATGACGGT
genomic: TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTAgtaagtacat ... tgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACA-GAACCCAGCTGCGAATGACGGT
EST: gi|4283486|gb|AI440662.1|AI440662
EST:     TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTA                         GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCT
genomic: TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTAgtaagtacat ... tgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCT
EST: gi|10231964|gb|BE800852.1|BE800852
EST:     TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTA                         GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
genomic: TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTAgtaagtacat ... tgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
EST: gi|151404341|gb|EV274151.1|EV274151
EST:     TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTA                         GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
genomic: TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTAgtaagtacat ... tgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
EST: gi|151400490|gb|EV270304.1|EV270304
EST:     TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTA                         GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
genomic: TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTAgtaagtacat ... tgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
EST: gi|51334703|gb|CO978569.1|CO978569
EST:     TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTA                         GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
genomic: TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTAgtaagtacat ... tgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
EST: gi|298170085|gb|HO018709.1|HO018709
EST:     TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTA                         GTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT
genomic: TTGTGAGTACAACATTTTATTCAGAAAGTACAAGGGCAATGCTTTGTTTAgtaagtacat ... tgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggcagttgataacatttttaaactcttgttttttttgtgaatgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA
          tgataac  putative branch site (score: 2)
            ataacatttttaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgccggtcattcatgattaaattgatgataacattagttgaaacttttggcagttgataacatttttaaactcttgttttttttgtgaatgatgtgcagGTAAGAATTGAAACAGATCCAGCAGACAGAACCCAGCTGCGAATGACGGTTGCTTCAGGGGACCCAACACTAACATTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
ctgccgg
- - - - cattcat
- - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - gcagttg