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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccccagacattgtcttcaattcctaccaataaaaaaaaatagatgttgatatgatttttggaattcaatattatcttactgtgtggttacgcatgtagACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATA

Basic information

species Glycine max
transcript GLYMA16G04560.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 5
-----atccccagacattgtcttcaattcctaccaataaaaaaaaatagatgttgatatgatttttggaattcaatattatcttactgtgtggttacgcatgtagACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATA
           | | |  ||  |    || |     | ||     |   || ||   |  |  | |||  ||   |  |   ||  ||||| |||   |    |||||||||||||||||||||||||||| || ||||| || || ||||| ||||| || ||||||||||| ||||| 
agaaggaaaaaaaaaaaagttatggtatctttggtttgaatgttcaaccatatttgaactaactgtggcttttgtttctgg-ttcttgtgttgttgaac----agACCATGGCATGGATACTAGATGAGTACTCGAAATTTCATGGCTACTCACCTGCTGTGGTGACTGGAAAGCCTATT
















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|7284551|gb|AW597139.1|AW597139
EST:     TTGGAACTCACACAGATGTGCCAGCACCTGATATGGGAACAGGACCACAG                         ACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCT
genomic: TTGGAACTCACACAGATGTGCCAGCACCTGATATGGGAACAGGACCACAGgtcagtacta ... acgcatgtagACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCT
EST: gi|192308765|gb|FG999790.1|FG999790
EST:     TTGGAACTCACACAGATGTGCCAGCACCTGATATGGGAACAGGACCACAG                         ACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCT
genomic: TTGGAACTCACACAGATGTGCCAGCACCTGATATGGGAACAGGACCACAGgtcagtacta ... acgcatgtagACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCT
EST: gi|4397421|gb|AI496418.1|AI496418
EST:     TTGGAACTCACACAGATGTGCCAGCACCTGATATGGGAACAGGGCCACAG                         ACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGNTACTCTCCT
genomic: TTGGAACTCACACAGATGTGCCAGCACCTGATATGGGAACAGGACCACAGgtcagtacta ... acgcatgtagACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCT
EST: gi|12496130|gb|BG046909.1|BG046909
EST:     TTGGAACTCACACAGATGTGCCAGCACCTGATATGGGAACAGGACCACAG                         ACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCT
genomic: TTGGAACTCACACAGATGTGCCAGCACCTGATATGGGAACAGGACCACAGgtcagtacta ... acgcatgtagACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCT
EST: gi|26058522|gb|CA801436.1|CA801436
EST:     TTGGAACTCACACAGATGTGCCAGCACCTGATATGGGAACAGGACCACAG                         ACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCT
genomic: TTGGAACTCACACAGATGTGCCAGCACCTGATATGGGAACAGGACCACAGgtcagtacta ... acgcatgtagACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCT
EST: gi|208192091|gb|GD992389.1|GD992389
EST:     CACCTGATATGGGAACAGGGCCACAG                         ACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCT
genomic: CACCTGATATGGGAACAGGACCACAGgtcagtacta ... acgcatgtagACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCT
EST: gi|10847674|gb|BF070321.1|BF070321
EST:     TGGAACTCACACAGATGTGCCAGCACCTGATATGGTAACAGGACTC-CAG                         ACTATGGCATGGATACTAGATGAGTATACCAAATTCC
genomic: TGGAACTCACACAGATGTGCCAGCACCTGATATGGGAACAGGAC-CACAGgtcagtacta ... acgcatgtagACCATGGCATGGATACTAGATGAGTATTCCAAATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgatatgatttttggaattcaatattatcttactgtgtggttacgcatgtagACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATA
                             atcttac  putative branch site (score: 3)
          atttttggaattcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atccccagacattgtcttcaattcctaccaataaaaaaaaatagatgttgatatgatttttggaattcaatattatcttactgtgtggttacgcatgtagACCATGGCATGGATACTAGATGAGTATTCCAAATTCCACGGTTACTCTCCTGCAGTAGTGACTGGAAAACCTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG