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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcaatcactagtgtgtgccttgaagtagctgtttttataacgtcgcatgggatgatgtagctaacacgttcactttgttataacccttccatttatagATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCATCTGAACTTGATGAACTATCTGGTCCTGATAAAGAACCAGCTAGAGAGT

Basic information

species Glycine max
transcript GLYMA01G22620.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G22620.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0011g02860.t01 (Vitis vinifera), 3'ss of exon 7
ttgcaatcactagtgtgtgccttgaagtagctgtt-tttataacgtcgcatgggatgatgt-agctaacacgttcactttgtta--taac-ccttccat-ttatagATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCATCTGAACTTGATGAACTATCTGGTCCTGATAAAGAACCAGCTAGAGAGT
     ||| |  |||  |      || |   | || ||| ||        ||| ||  | | | | ||     |||    || |  |||    |||||| ||  |||| || ||||| ||||||||||||||||  ||||||||||| |||||  |||| || ||||||| |||   ||| || || || ||||||    ||||||
-----atc-catgtgattaaacaaaactctttcttctttgtatgaatatgtggaatcctatcaaccaatgttatcaaacggtaaaataatattttccatcttgcagATTAAACTTTCGTCTGTACAACTGGCAAGAAAGTATATGAAGCGTGTATCATCAGAGCTTGATGCACTGAGTGGACCAGAGAAGGAACCAAACCGAGAGT
















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|6134519|gb|AW132912.1|AW132912
EST:     TGGATTCAGGGGTTGTAGGCAAG                         ATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCA
genomic: TGGATTCAGGGGTTGTAGGCAAGgtatgcttct ... ccatttatagATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCA
EST: gi|192294897|gb|FG987586.1|FG987586
EST:     AATTTGGAATCCCAGTGAACTGGCTAATGGATTCAGGGGTTGTAGGCAAG                         ATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCA
genomic: AATTTGGAATCCCAGTGAACTGGCTAATGGATTCAGGGGTTGTAGGCAAGgtatgcttct ... ccatttatagATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCA
EST: gi|105634535|gb|DW247584.1|DW247584
EST:     AATTTGGAATCCCAGTGAACTGGCTAATGGATTCAGAGGTTGTAGGCAAG                         ATCAAGCTTTCTTCTGT
genomic: AATTTGGAATCCCAGTGAACTGGCTAATGGATTCAGGGGTTGTAGGCAAGgtatgcttct ... ccatttatagATCAAGCTTTCTTCTGT
EST: gi|5760036|gb|AI965399.1|AI965399
EST:     AATTTGGAATCCCAGTGAACTGGCTAATGGATTCAGGGGTTGTAGGCAAG                         ATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCA
genomic: AATTTGGAATCCCAGTGAACTGGCTAATGGATTCAGGGGTTGTAGGCAAGgtatgcttct ... ccatttatagATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCA
EST: gi|192309845|gb|FK001389.1|FK001389
EST:     AATTTGGAATCCCAGTGAACTGGCTAATGGATTCAGGGGTTGTAGGCAAG                         ATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCA
genomic: AATTTGGAATCCCAGTGAACTGGCTAATGGATTCAGGGGTTGTAGGCAAGgtatgcttct ... ccatttatagATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcatgggatgatgtagctaacacgttcactttgttataacccttccatttatagATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCATCTGAACTTGATGAACTATCTGGTCCTGATAAAGAACCAGCTAGAGAGT
                                  ttataac  putative branch site (score: 2)
                                        cccttccattt  CT-rich tract
                              tttgttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcaatcactagtgtgtgccttgaagtagctgtttttataacgtcgcatgggatgatgtagctaacacgttcactttgttataacccttccatttatagATCAAGCTTTCTTCTGTACAACTGGCAAAGAAGTATATGAAACGTGTTGCATCTGAACTTGATGAACTATCTGGTCCTGATAAAGAACCAGCTAGAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- -caatcac
- - - - - - gtgtgtg
- - - - - - - - - -ccttgaa
- - - - - - - - - - - - - gtagctg
- - - - - - - - - - - - - - - - - - - - - - - gcatggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaacac