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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgtcaaaaccttgttttatataggttgccataatttgtcatacaactgatttgtgctctttcatttttccttgttttactgcagACACAAATTGTTAGTGATGAAACTTGGAAATTAGTAGATGATATCTGGGATAAAAAGGTTCAAAACATTAAAGATGAAGCTTCAATGGTGATTGAAGAAG

Basic information

species Glycine max
transcript GLYMA04G39180.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39180.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv04s0044g01180.t01 (Vitis vinifera), 3'ss of exon 15
------gtatatgtcaaaaccttgttttatataggttg-ccataatttgtcat-acaactgatttgtgctctttcatttttccttgttttactgcagACACAAATTGTTAGTGATGAAACTTGGAAATTAGTAGATGATATCTGGGATAAAAAGGTTCAAAACATTAAAGATGAAGCTTCAATGGTGATTGAAGAAG
        | | ||    | |||  | | |     ||| | ||||||| | || ||| ||||    ||||  ||   | |||| | |||   ||||||| |||||  | |||||||||||||||||| || | |||| |||||||||||||| ||||||  | ||||||| |||||| |||||     |||||||||
gtaagcagaaaagtactcatcttagtctttgccatttgactataatttattatgacagctga----tgctggtt---tcttccatttttatatgcagACTCAAATCATCAGTGATGAAACTTGGAAACTAATCGATGGTATCTGGGATAAAAGGGTTCAGGAAATTAAAGCTGAAGCCTCAATCCAAGTTGAAGAAG
















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|20815035|gb|BQ299513.1|BQ299513
EST:     GATTTGCGACCTTTGGTGCACCTCGCCCTACAGAG                         ACACAAATTGTTAGTGATGAAACTTGGAAATTAGTAGATGATATCTGGGAT
genomic: GATTTGCGACCTTTGGTGCACCTCGCCCTACAGAGgtatatgtca ... tttactgcagACACAAATTGTTAGTGATGAAACTTGGAAATTAGTAGATGATATCTGGGAT
EST: gi|51343629|gb|CO984362.1|CO984362
EST:     GGATTTGCGACCTTTGGTGCACCTCGCCCTACAGAG                         ACACAAATTGTTAGTGATGAAACTTGGAAATTAGTAGATGATATCTGGGAT
genomic: GGATTTGCGACCTTTGGTGCACCTCGCCCTACAGAGgtatatgtca ... tttactgcagACACAAATTGTTAGTGATGAAACTTGGAAATTAGTAGATGATATCTGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatttgtcatacaactgatttgtgctctttcatttttccttgttttactgcagACACAAATTGTTAGTGATGAAACTTGGAAATTAGTAGATGATATCTGGGATAAAAAGGTTCAAAACATTAAAGATGAAGCTTCAATGGTGATTGAAGAAG
              aactgat  putative branch site (score: 3)
                    tttgtgctctttcatt  CT-rich tract
                             tttcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgtcaaaaccttgttttatataggttgccataatttgtcatacaactgatttgtgctctttcatttttccttgttttactgcagACACAAATTGTTAGTGATGAAACTTGGAAATTAGTAGATGATATCTGGGATAAAAAGGTTCAAAACATTAAAGATGAAGCTTCAATGGTGATTGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG