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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatattaaaaaaaaatgcatatactagtgttgtgaaagctgaataacttagttttttttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGAC

Basic information

species Glycine max
transcript GLYMA01G39330.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39330.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G36960.2 (Arabidopsis thaliana), 3'ss of exon 9
-------------gtaagatattaaaaaaaaatgcatatactagtgttgtgaaagctgaat--aacttagttttttttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGAC
             || | ||  | | |   |   ||| | |   | || |   |  || ||  ||| |   |  ||||||   ||||| || |||||||  || ||||||||||||||||||||||| ||||||||| ||||||| |||||||| ||  | ||||| |||||||| || |||||||
gtgagttatataagttacattgttacactgagaacattttcagatatttttgtatatgtattgaacattcatccttttttaattagGACCCAAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGAC

upper sequence: GLYMA01G39330.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv07s0031g00600.t01 (Vitis vinifera), 3'ss of exon 11
-----------gtaagat-attaaaaaaaaatgcatatactagtgttgtgaaagct--gaataacttagttttttttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGAC
            |||  | ||||    |  |   ||| |    |     | ||  |   || |    | | ||  ||||  |||||||||||||||||  || ||||| || ||||| ||||| || |||||||||||||||||||| ||||| || ||||||||||||||||||||||| ||||
gtaaattagagataaacttattattctaccaccaatagatggattcaaggtaacttcaaaacagaggaatattcattttatgtagGATCCTAAGAGAAGTGGCCATAGGGGCTTTGGTTTTGTAACCTTTGCTGAAGATGGTGTAGCTGATCGTGTATCTCGAAGGTCTCATGAGATTTGCGGAC
















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|58020024|gb|CX706766.1|CX706766
EST:     GTCAATATTTTGGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGG                         GATCTTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
genomic: GTCAATATTTTGGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGGgtaagatatt ... ttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
EST: gi|58023593|gb|CX710334.1|CX710334
EST:     GTCAATATTTTGGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGG                         GATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
genomic: GTCAATATTTTGGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGGgtaagatatt ... ttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
EST: gi|254318602|gb|GR832770.1|GR832770
EST:     GTCAATATTTTGGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGG                         GATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
genomic: GTCAATATTTTGGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGGgtaagatatt ... ttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
EST: gi|58024913|gb|CX711654.1|CX711654
EST:     GTCAATATTTTGGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGG                         GATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
genomic: GTCAATATTTTGGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGGgtaagatatt ... ttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
EST: gi|254337734|gb|GR845304.1|GR845304
EST:     TCAATATTTTGGGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGG                         GATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
genomic: TCAATATTTT-GGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGGgtaagatatt ... ttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
EST: gi|58020404|gb|CX707146.1|CX707146
EST:     GTCAATATTTTGGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGG                         GATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
genomic: GTCAATATTTTGGAAGATTTGGTCGTATATTAGATGTTTATGTTCCAAGGgtaagatatt ... ttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
EST: gi|18711451|gb|BM522593.1|BM522593
EST:     TAGATGTTTATGTTCCAAGG                         GATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA
genomic: TAGATGTTTATGTTCCAAGGgtaagatatt ... ttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgcatatactagtgttgtgaaagctgaataacttagttttttttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGAC
                            gaataac  putative branch site (score: 2)
                                  cttagtttttttttt  CT-rich tract
                           tgaataacttagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatattaaaaaaaaatgcatatactagtgttgtgaaagctgaataacttagttttttttttgggtagGATCCTAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT