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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgcatataatgtactttatactttcatttttctttgatgactaaaagcttctagtgttttgataagtttccccatttttttaaaaataaactcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTAGTGATTAGGCCCATGTACTCAAGTCCTCCTATTCATGGTGCATCCATTG

Basic information

species Glycine max
transcript GLYMA04G08560.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G08560.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 8
gcgcatataatgtactttatactttcatttttctttgatgactaaa-agcttctagtgttttgataagtttccccatttttttaaaaataaactcacct--------agGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTAGTGATTAGGCCCATGTACTCAAGTCCTCCTATTCATGGTGCATCCATTG
          |  |  ||| | ||| ||| |   |||||| | |   || |  || | |  |  | |||| |          | ||   ||  | || |        |||| ||       |||||||| ||   |||||| || || || || || || || |||||||| ||||| ||||  |||||||||||||||||||| || |
---------gttgaaattaaattttgattctaagttgatgccgacccagataataatatcctatttagttgcatagaaaaactgaacggaatgtaactttgtatttcagGTTTGTGGAAGTGCTGATGTAGCTGTCAGGGTTGAAAGTCAACTTAAGCTTGTAATTAGGCCTATGTATTCAAACCCTCCTATTCATGGTGCATCTATCG
















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|192306581|gb|FG996243.1|FG996243
EST:     ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATT                         GTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
genomic: ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATTgtaagaactt ... actcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
EST: gi|20812962|gb|BQ297440.1|BQ297440
EST:     ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATT                         GTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
genomic: ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATTgtaagaactt ... actcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
EST: gi|192328739|gb|FK023197.1|FK023197
EST:     GGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATT                         GTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
genomic: GGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATTgtaagaactt ... actcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
EST: gi|22932102|gb|BU549241.1|BU549241
EST:     ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATN                         GTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
genomic: ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATTgtaagaactt ... actcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
EST: gi|192334120|gb|FK026277.1|FK026277
EST:     ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATT                         GTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
genomic: ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATTgtaagaactt ... actcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
EST: gi|17153142|gb|BM143075.1|BM143075
EST:     ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATT                         GTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
genomic: ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATTgtaagaactt ... actcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
EST: gi|254322787|gb|GR839808.1|GR839808
EST:     GGGAACGTGTTGGCGCCTTAAGCATT                         GTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
genomic: GGGAACGTGTTGGCGCCTTAAGCATTgtaagaactt ... actcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTA
EST: gi|17153235|gb|BM143168.1|BM143168
EST:     ATGCAAAGAATCTGCGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATT                         GTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACT
genomic: ATGCAAAGAATCTGGGTCTTTATGGGGAACGTGTTGGCGCCTTAAGCATTgtaagaactt ... actcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcttctagtgttttgataagtttccccatttttttaaaaataaactcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTAGTGATTAGGCCCATGTACTCAAGTCCTCCTATTCATGGTGCATCCATTG
                                            aactcac  putative branch site (score: 2)
                                              ctcacct  CT-rich tract
                             atttttttaaaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgcatataatgtactttatactttcatttttctttgatgactaaaagcttctagtgttttgataagtttccccatttttttaaaaataaactcacctagGTCTGCAAGTCAGCTGATGTTGCAAGCAGGGTCGAGAGCCAGCTGAAACTAGTGATTAGGCCCATGTACTCAAGTCCTCCTATTCATGGTGCATCCATTG

- - - - aatgtac
- - - - - - - - - - - - - - - - - -tgatgac
- - - - - - - - - - - - - - - - - - - - - - - -gcttcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa