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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatttggaatgcttacatgattactttttttcttttttattcatgtagggtgtttgtttacttttggtgttaacattgtttttattctaaatctaacagAGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAAGGTGCCCTTACACCTGAAGAAATAGCTAAG

Basic information

species Glycine max
transcript GLYMA01G38270.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G38270.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g01820.t01 (Vitis vinifera), 3'ss of exon 4
ccatttggaatgcttacatgattactttttttcttttttattcatgtagggtgtttgtttacttttggtgt-taacattgttt-ttattctaaatc-taacagAGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAAGGTGCCCTTACACCTGAAGAAATAGCTAAG
  ||  | || | ||   | |   |    |||  ||  |    || |||      |  |  ||     ||| |||||  | |  ||||| |   |  | ||||||||| || |||||||| || |||||| |||||||||| || || ||||| || || |||||||| | |||||||||||||
-tatgagaaaaggttt--ttacagcagaattttcttactcagaatatagccctgcttatggctgaaaatgtataacagagctccttattttgccttatgacagAGGCTGTCGGGAGCATCCTTGCTGATACTAGCAAATAAGCAAGATATAAATGGAGCTCTTACACCAGCAGAAATAGCTAAG
















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|12773243|gb|BG238170.1|BG238170
EST:     GAAGGTTGGATGATTGCAAATTCGAGCTCGATAACCTTCTCAAGGAAGAG                         AGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAA
genomic: GAAGGTTGGATGATTGCAAATTCGAGCTCGATAACCTTCTCAAGGAAGAGgtttgttcta ... aatctaacagAGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAA
EST: gi|4277030|gb|AI431194.1|AI431194
EST:     GAAGGTTGGATGATTGCAAATTCGAGCTCGATAACCTTCTCAAGGAAGAG                         AGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAA
genomic: GAAGGTTGGATGATTGCAAATTCGAGCTCGATAACCTTCTCAAGGAAGAGgtttgttcta ... aatctaacagAGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAA
EST: gi|51336376|gb|CO980242.1|CO980242
EST:     GAAGGTTGGATGATTGCAAATTCGAGCTCGATAACCTTCTCAAGGAAGAG                         AGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAA
genomic: GAAGGTTGGATGATTGCAAATTCGAGCTCGATAACCTTCTCAAGGAAGAGgtttgttcta ... aatctaacagAGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAA
EST: gi|151404450|gb|EV274264.1|EV274264
EST:     GAAGGTTGGATGATTGCAAATTCGAGCTCGATAACCTTCTCAAGGAAGAG                         AGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAA
genomic: GAAGGTTGGATGATTGCAAATTCGAGCTCGATAACCTTCTCAAGGAAGAGgtttgttcta ... aatctaacagAGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagggtgtttgtttacttttggtgttaacattgtttttattctaaatctaacagAGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAAGGTGCCCTTACACCTGAAGAAATAGCTAAG
                                        ttctaaa  putative branch site (score: 2)
                         ttaacattgtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatttggaatgcttacatgattactttttttcttttttattcatgtagggtgtttgtttacttttggtgttaacattgtttttattctaaatctaacagAGGCTATCTGGAGCATCTTTACTGATATTAGCAAATAAACAGGACATAAAAGGTGCCCTTACACCTGAAGAAATAGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
ccatttg
- - - -gaatgct
- - - - - - - tacatga
- - - - - - - - - - - - - - - - - - - - -tcatgta
- - - - - - - - - - - - - - - - - - - - - - - - gggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttggtg