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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagactaagacaaagacattcattttaacgaagactcaaaattgttccattttttttttacatgtgatctgaatgaaattaaaattttgacgacactgaagCGAGGATAAAGGTTTACGAGCTTAGGAACAAGACGAAGGCGGAGCTGCTGAACCAGCTGAAGGATCTCAAGGCGGAGCTTGCCCTGCTCCGCGTCGCCAA

Basic information

species Glycine max
transcript GLYMA10G05270.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G05270.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g30730.1 (Oryza sativa), 3'ss of exon 1
gtaagactaagacaaagacattcattttaacgaagactcaaaattgttccattttttttttacatgtgatctgaatgaaattaaaattttgacgacactgaagCGAGGATAAAGGTTTACGAGCTTAGGAACAAGACGAAGGCGGAGCTGCTGAACCAGCTGAAGGATCTCAAGGCGGAGCTTGCCCTGCTCCGCGTCGCCAA
||||| ||    |        ||    |  |   |  |||   | | |   ||||   | |  ||    || | ||   |       || ||| | |    |||  |||| |||||  |||||||  ||   ||||  ||||||||||||| |  |||||| ||||| ||||||||||||||  |||| ||||||||||||||
gtaagcctccccc-----tcctctccctctctccggttcatc-tcgattagttttagctctcaatcccttccggatctgaccgtttcttggacaa-atgtcagCCCGGATCAAGGTGCACGAGCTCCGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA

upper sequence: GLYMA10G05270.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g30050.1 (Oryza sativa), 3'ss of exon 1
gtaagactaagacaaagacattcattttaacgaagactcaaaattgttccattttttttttacatgtgatctgaatgaaattaaaattttgacgacactgaagCGAGGATAAAGGTTTACGAGCTTAGGAACAAGACGAAGGCGGAGCTGCTGAACCAGCTGAAGGATCTCAAGGCGGAGCTTGCCCTGCTCCGCGTCGCCAA
                                |||   ||| |||      || | |  |  |    |  |||   | |  |||   |  |       || |||  |||| |||||  |||||||  ||   ||||  ||||||||||||| |  |||||| ||||| ||||||||||||||  |||| ||||||||||||||
------------------------------gtaagctacaacattccgttcttctctcctcccgctcg-cctg--cggatctaaccgtgcgtgtgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA
















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|26268369|gb|CA819432.1|CA819432
EST:     GTTGCAGAGCTGCGCGTCGATCTAGAAAATGG                         CGAGGATAAAGGTTTACGAGCTTAGGAACAAGACGAAGGCGGAGCTGCTGA
genomic: GTTGCAGAGCTGCGCGTCGATCTAGAAAATGGgtaagactaa ... gacactgaagCGAGGATAAAGGTTTACGAGCTTAGGAACAAGACGAAGGCGGAGCTGCTGA
EST: gi|209709934|gb|BW670977.1|BW670977
EST:     TGCGCGTCGATCTAGAAAATGG                         CGAGGATAAAGGTTTACGAGCTTAGGAACAAGACGAAGGCGGAGCTGCTGA
genomic: TGCGCGTCGATCTAGAAAATGGgtaagactaa ... gacactgaagCGAGGATAAAGGTTTACGAGCTTAGGAACAAGACGAAGGCGGAGCTGCTGA
EST: gi|10255379|gb|BE823145.1|BE823145
EST:     GCGCGTCGATCTAGAAAATGG                         CGAGGATAAAGGTTTACGAGCTTAGGANNAAGACGAAGGCGGAGCTGCTGA
genomic: GCGCGTCGATCTAGAAAATGGgtaagactaa ... gacactgaagCGAGGATAAAGGTTTACGAGCTTAGGAACAAGACGAAGGCGGAGCTGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattttttttttacatgtgatctgaatgaaattaaaattttgacgacactgaagCGAGGATAAAGGTTTACGAGCTTAGGAACAAGACGAAGGCGGAGCTGCTGAACCAGCTGAAGGATCTCAAGGCGGAGCTTGCCCTGCTCCGCGTCGCCAA
                                      ttttgac  putative branch site (score: 3)
                    atctgaatgaaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagactaagacaaagacattcattttaacgaagactcaaaattgttccattttttttttacatgtgatctgaatgaaattaaaattttgacgacactgaagCGAGGATAAAGGTTTACGAGCTTAGGAACAAGACGAAGGCGGAGCTGCTGAACCAGCTGAAGGATCTCAAGGCGGAGCTTGCCCTGCTCCGCGTCGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT