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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttctctgtttttttttttttgttgttgttgttctgatgaaaatctcgtgaacttgtgtgcatttgctttcactcattgttgattaaacgcgtatgattattctaatttttaaaccattgttatgtgaagAATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAAGAGGAACGAGGAGTGGGCTTTGGAGAAGAAGCAGGAACTCGATGCCGCA

Basic information

species Glycine max
transcript GLYMA09G06860.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgagtttttctctgtttttttttttttgttgttgttgttctgatgaaaatctcgtgaacttgtgtgcatttgctt-tcactcattgttgattaaacgcgtatgatt-attctaatttttaaaccattgttatgtgaagAATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAAGAGGAACGAGGAGTGGGCTTTGGAGAAGAAGCAGGAACTCGATGCCGCA
                                             |  | | ||||  | |    |   |   ||  |||   || | |   |   ||   || ||| | |||   || |  | |      ||  | | |||||  ||  | ||||   | ||||| || |||||| ||||||||  ||||||  | ||||| ||||||||||||||||||||| |  | |        
---------------------------------------------gttagtgtcgtcgagtctcttctctccactcatcatctatcgatttatcgtcgttaatcattgaatctgggttgttgatctgcagGATTCGGA-AATGGTTGAGTCAAAGGTTGTAGTTCCAGAGTCGGTGTTGAAGAAGAGGAAGAGAGAGGAGGAATGGGCTTTGGAGAAGAAGCAGAATGTTG--------
















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|298191259|gb|HO038738.1|HO038738
EST:     ACGACCCTCCGCCGCCGCGGTTGCAAGCAGAGCACACCATCGA                         AATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA
genomic: ACGACCCTCCGCCGCCGCGGTTGCAAGCAGAGCACACCATCGAgtgagttttt ... ttatgtgaagAATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA
EST: gi|208235102|gb|GE029596.1|GE029596
EST:     ACCCTCCGCCGCCGCGGTTGCAAGCAGAGCACACCATCGA                         AATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA
genomic: ACCCTCCGCCGCCGCGGTTGCAAGCAGAGCACACCATCGAgtgagttttt ... ttatgtgaagAATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA
EST: gi|298175439|gb|HO015072.1|HO015072
EST:     GACCCTCCGCCGCCGCGGTTGCAAGCAGAGCACACCATCGA                         AATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA
genomic: GACCCTCCGCCGCCGCGGTTGCAAGCAGAGCACACCATCGAgtgagttttt ... ttatgtgaagAATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA
EST: gi|192302636|gb|FG994888.1|FG994888
EST:     GCCGCCGCGGTTGCAAGCAGAGCACACCATCGA                         AATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA
genomic: GCCGCCGCGGTTGCAAGCAGAGCACACCATCGAgtgagttttt ... ttatgtgaagAATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA
EST: gi|209706672|gb|BW676168.1|BW676168
EST:     ACGAGCCTCCGCCGCCGCGGTTGCAAGCAGAGCACACCATCGA                         AATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA
genomic: ACGACCCTCCGCCGCCGCGGTTGCAAGCAGAGCACACCATCGAgtgagttttt ... ttatgtgaagAATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA
EST: gi|192307307|gb|FK001265.1|FK001265
EST:     ACCACTCACGACCCTCCGCCGCCGCGGTTGCAAGCAGAGCACACCATCGA                         AATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA
genomic: ACCACTCACGACCCTCCGCCGCCGCGGTTGCAAGCAGAGCACACCATCGAgtgagttttt ... ttatgtgaagAATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttgattaaacgcgtatgattattctaatttttaaaccattgttatgtgaagAATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAAGAGGAACGAGGAGTGGGCTTTGGAGAAGAAGCAGGAACTCGATGCCGCA
                         ttctaat  putative branch site (score: 2)
                     attattctaattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttttctctgtttttttttttttgttgttgttgttctgatgaaaatctcgtgaacttgtgtgcatttgctttcactcattgttgattaaacgcgtatgattattctaatttttaaaccattgttatgtgaagAATGGGCGAAGCGAAGGCGTTGGTTCCGGAATCGGTGGTGAAGAAGGAGAAGAGGAACGAGGAGTGGGCTTTGGAGAAGAAGCAGGAACTCGATGCCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC