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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccctctccaatcccttcttcccttacaatttttttcttttcttttctggatcttaattttggattctcgacctagctagggtttatcgctgcgcttgttgagattgtaacactaattcgcgtttgtttgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTCGAGCCTAGGCCTCCGTTGGAGTACAAGCCACCTCCGGAGAAACGAAAAT

Basic information

species Glycine max
transcript GLYMA11G07200.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07200.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g01580.t01 (Vitis vinifera), 3'ss of exon 1
gtccctctccaatcccttcttcccttacaatttttttcttttcttttctggatcttaattttggattctcgacctagctagggtttatcgctgcgcttgttgagattgtaacactaattcgcgtttgtttgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTCGAGCCTAGGCCTCCGTTGGAGTACAAGCCACCTCCGGAGAAACGAAAAT
                                      | | || |  || |  || ||   ||| |   ||   |   |   ||| | | |          ||  ||    | |   |     ||| ||||||||||||| || |||||||| || |||||||| ||||| || || ||||| ||||| |||||| | ||||| |||||||  || |||||||| |||||| ||||||
-----------------------------------gcttgtcctgtcgtgtagatttatcaaggaatt--gaagaaatcattcttt-ttgtttaatggacataggctgagttattttatta-aattgcttgttatgcagATCGGGCAGAGTCATCCCACCGGTCTAACAGCCAATCTTTTGAAACTCTTTGAGCCTCGTCCTCCATTGGAGTTTAAACCACCTCCAGAGAAAAGAAAAT

upper sequence: GLYMA11G07200.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S332_45V6.1 (Physcomitrella patens), 3'ss of exon 1
gtccctctccaatcccttcttcccttacaatttttttcttttcttttctggatcttaattttggattctcgacctagctagggtttatcgctgcgcttgttgagattgtaacacta-attcgcgtttgtttgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTCGAGCCTAGGCCTCCGTTGGAGTACAAGCCACCTCCGGAGAAACGAAAAT
                                         ||  |   || ||| |  |  | | | |       | ||||   | ||     | ||||    | || |  |  | ||||   |  ||||| |   |||||||| ||||| || ||||| ||| | ||  | || || |||||||| ||||||||||||||||| ||||| | |||||| ||||| || || ||||| |
----------------------------------gaaagggtcgatgtcggttctgatgtacgaaatattatgtgtggtaggtgctttca----ggttgtgcgaaatggactaacacattcttatccgtttgctt--cagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTCGAGCCTAGGCCTCCTTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGT

upper sequence: GLYMA11G07200.2 (Glycine max), 3'ss of exon 1
lower sequence: EFJ17734 (Selaginella moellendorffii), 3'ss of exon 1
gtccctctccaatcccttcttcccttacaatttttttcttttcttttctggatcttaattttggattctcgacctagctagggtttatcgctgcgcttgttgagattgtaacactaattcgcgtttgtttgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTCGAGCCTAGGCCTCCGTTGGAGTACAAGCCACCTCCGGAGAAACGAAAAT
                                                                                |    | |||   ||| | ||    |||     ||  |  ||  || | |    | ||||| || ||||| || || |||||  | || ||||| || |||||||||||||||||  |||||||  | ||||||||||| || |||||||| || ||  
--------------------------------------------------------------------------------gtaagtctcgtctcgcctcttctctttgatcggcttctcagcccttttct----ttcagATCGGCCAGAGCCATCCCACCGGATTGACTGCGAATCTTTTGAAGCTCTTCGAGCCGCGGCCTCCTCTCGAGTACAAGCCGCCGCCGGAGAAGCGGAATC

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|209727268|gb|BW655253.1|BW655253
EST:     AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTG                         ATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
genomic: AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTGgtccctctcc ... tgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
EST: gi|209728976|gb|BW655019.1|BW655019
EST:     AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTG                         ATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
genomic: AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTGgtccctctcc ... tgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
EST: gi|209698445|gb|BW667242.1|BW667242
EST:     AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTG                         ATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
genomic: AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTGgtccctctcc ... tgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
EST: gi|11412754|gb|BF424765.1|BF424765
EST:     AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTG                         ATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
genomic: AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTGgtccctctcc ... tgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
EST: gi|213603451|gb|DB970492.1|DB970492
EST:     AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTG                         ATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
genomic: AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTGgtccctctcc ... tgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
EST: gi|18039679|gb|BM307973.1|BM307973
EST:     AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTG                         ATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
genomic: AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTGgtccctctcc ... tgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
EST: gi|213618444|gb|DB963373.1|DB963373
EST:     AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTG                         ATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
genomic: AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTGgtccctctcc ... tgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
EST: gi|8826552|gb|BE210282.1|BE210282
EST:     AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTG                         ATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC
genomic: AGGCCCGCACCAAAGCGCAGAACCGCTCCAACGTCCTTCAGCTCAAACTGgtccctctcc ... tgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatcgctgcgcttgttgagattgtaacactaattcgcgtttgtttgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTCGAGCCTAGGCCTCCGTTGGAGTACAAGCCACCTCCGGAGAAACGAAAAT
                           cactaat  putative branch site (score: 2)
                                       tttgttt  putative PPT
                                           tttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccctctccaatcccttcttcccttacaatttttttcttttcttttctggatcttaattttggattctcgacctagctagggtttatcgctgcgcttgttgagattgtaacactaattcgcgtttgtttgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTCGAGCCTAGGCCTCCGTTGGAGTACAAGCCACCTCCGGAGAAACGAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA