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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtatttgaaggattaatttcgttttgatcgcgatgatttgggaactgtaggtgactcattctttatttattgatgctcttttttgtggtgccgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGG

Basic information

species Glycine max
transcript GLYMA13G27600.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G27600.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 1
ttttgtatttgaaggattaatttcgttttgatcgcgatgatttgggaactgtaggtgactcattctttatttattgatgctcttttttgtggtgccgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGG
 |  ||  |||   | ||| |  ||  |   |   |  | | |  ||| |       | |     || || |  ||||  | ||| || ||      ||||| || ||||| ||| |  | || ||||| || | | | |||||||||||||| || | |||||| || ||||||||||||||||| || || || ||||
gtacgtgcttgcttgcttattcgcgaatcttttttggggttctctgaaattctctaaattagggtttcatattctgattgtttttgttttg------cagATCATATCTCCATATAACCTTTATTTGAATCCGACACTTGTGGTGAAGCAATACCAATATTGGCGTCTCGTTACTAATTTCTTGTATTTCCGGAAGATGG
















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|192308645|gb|FG999726.1|FG999726
EST:     GCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAA
genomic: GCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGATgtaaaccccc ... ggtgccgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAA
EST: gi|192327521|gb|FK018197.1|FK018197
EST:     GCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAA
genomic: GCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGATgtaaaccccc ... ggtgccgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAA
EST: gi|298194426|gb|HO041074.1|HO041074
EST:     GCTCTTATCTCACCGCTGCTGTTGTCACCACCATCGGATGTTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTAGATTGGTGGTGAAGCAA
genomic: GCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGATgtaaaccccc ... ggtgccgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAA
EST: gi|192319097|gb|FK010633.1|FK010633
EST:     GCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAA
genomic: GCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGATgtaaaccccc ... ggtgccgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAA
EST: gi|192305754|gb|FG995710.1|FG995710
EST:     GCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAA
genomic: GCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGATgtaaaccccc ... ggtgccgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAA
EST: gi|192294844|gb|FG987533.1|FG987533
EST:     GCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGAT                         ATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAA
genomic: GCTCCTATCTCACCGCTGCTGTTGTCACCACTATCGGATGCTCCCTTGATgtaaaccccc ... ggtgccgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactgtaggtgactcattctttatttattgatgctcttttttgtggtgccgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGG
                          tattgat  putative branch site (score: 3)
                attctttatttattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtatttgaaggattaatttcgttttgatcgcgatgatttgggaactgtaggtgactcattctttatttattgatgctcttttttgtggtgccgcagATAATTTCTCCGTATCATTTGTACTTGAACCCTATATTGGTGGTGAAGCAATATCAGTTTTGGCGCCTGGTTACTAATTTCTTGTACTTTCGTAAAATGG

- - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgct