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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatattcttgctggccatgtactctgaggtcattttattgtgctttgttttatggaaagacaactttacctttttctcttcttttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTC

Basic information

species Glycine max
transcript GLYMA13G17200.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G17200.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 5
---------gttatattcttgctggccatgtactctgagg-tcattttattg--tgctttgttttatggaaagacaactttacctttt--tctcttcttttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTC
          || | |  ||     |  | |  |||||   |   |  | |   | |  ||||   |   |  ||||  | |   |      || ||||| | || ||||||| |  ||||||||||| ||||| ||||| ||||||||||||||||| ||| ||| ||| || |||||||| |||||||| |||||
gtatatatatttgtttattttggtacatttttttctgaaaattggtccagtaatttccctgttccttttcattacaaactgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC

upper sequence: GLYMA13G17200.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ13606 (Selaginella moellendorffii), 3'ss of exon 5
gttatattcttgctggccatgtactctgaggtcattttattgtgctttgttttatggaaagacaactttacctttttctcttcttttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTC
                                       |||| ||||   || ||     |   || |    || ||   |        | |||| || |  ||||||||||| ||||| |||||||||||||| |||||||| ||| | || |||   ||||   | |||||| |||||||
--------------------------------------gttgtacttttaattttgttttcatttctctgagattatcgtct-------gtccagGACATTACAATATTTTTGTGGGTGATCTTAGTCCTGAGGTCACAGATGCAACACTCTACGCTGCTTTCTTCATGTATCCTGGTTGTTC

upper sequence: GLYMA13G17200.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28907 (Selaginella moellendorffii), 3'ss of exon 5
gttatattcttgctggccatgtactctgaggtcattttattgtgctttgttttatggaaagacaactttacctttttctc---ttcttttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTC
                                                ||| ||     |      ||| | ||| |||    || |  |   |||||| || |  ||||||||||| ||||| |||||||||||||| |||||||| ||| | || |||   ||||   | |||||| |||| ||
------------------------------------------------gttgtacttttaatttttttttcatttctctgagattatcgtctgttcagGACATTACAATATTTTTGTGGGTGATCTTAGTCCTGAGGTCACAGATGCAACACTCTACGCTGCTTTCTTCATGTATCCTGGTTGCTC

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|208327271|gb|GE122409.1|GE122409
EST:     TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAG                         GTCACTTTAATAATTTTTAGTCGGTGACCTTAGTC
genomic: TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAGgttatattct ... ttggattcagGTCACTTTAATA-TTTTT-GTCGGTGACCTTAGTC
EST: gi|193545482|gb|FK503989.1|FK503989
EST:     TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAG                         GTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGNTGCGA
genomic: TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAGgttatattct ... ttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGA
EST: gi|13252197|gb|BG363100.1|BG363100
EST:     TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAG                         GTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGA
genomic: TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAGgttatattct ... ttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGA
EST: gi|13789938|gb|BG652529.1|BG652529
EST:     TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAG                         GTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGA
genomic: TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAGgttatattct ... ttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGA
EST: gi|19348273|gb|BM892805.1|BM892805
EST:     TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAG                         GTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGA
genomic: TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAGgttatattct ... ttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGA
EST: gi|193355897|gb|FK319124.1|FK319124
EST:     TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAG                         GTCACTTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCG
genomic: TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAGgttatattct ... ttggattcagGTCACTTT-AATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCG
EST: gi|42723064|gb|CK768963.1|CK768963
EST:     TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAG                         GTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGA
genomic: TATTAAGGTTAACTGGGCTTATGCTAGCAGCCAGAGAGAGGATACCTCAGgttatattct ... ttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgctttgttttatggaaagacaactttacctttttctcttcttttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTC
                         ctttacctttttctct  CT-rich tract
     tttgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatattcttgctggccatgtactctgaggtcattttattgtgctttgttttatggaaagacaactttacctttttctcttcttttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG