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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgggtagtcctttttcggagttcatttgtattttctttaatcctagatcagtatttcccacttttctaactcgtgtgcatgtgctttgtgtggatgccagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACGTGGCTGGGGAGTGGAACCACACCTCTGGTCAATGGAATGGAGACGCTAA

Basic information

species Glycine max
transcript GLYMA10G28890.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 1
----cgggtagtcctttttcggagttcatttgtattttctttaatcctagatcagtatttcccacttttctaactcgtgtgcatgtgctttgtgtggatgc-cagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACGTGGCTGGGGAGTGGAACCACACCTCTGGTCAATGGAATGGAGACGCTAA
    | | || |   ||| ||   | ||||||    ||||  |   |  |||        |      ||||   |  | |  ||||  | | | ||  ||| |||| || ||||||| ||| ||||| || ||||| ||||| || ||||||||| ||||||| || ||||||||||| |||||  | |||||||||||  || |
cgggcagataatgaatttgcgtgat-catttgctggttctgca---catgatgcactgaacatggagttctgtgttatctaaatgtattctat-tgtgtgcacagATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGA

upper sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 1
-cgggtagtcctttttcggagttcatttgtattttctttaatcctagatcagtatttcccacttttctaactcgtgtgcatgtgctttgt-gtggatgccagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACGTGGCTGGGGAGTGGAACCACACCTCTGGTCAATGGAATGGAGACGCTAA
   ||   |||  |   |    ||| || | || |          |  |  ||| ||   || || |    || ||    | |||  ||| |||   |||||| || ||||||| ||| ||||| || || || ||||| || ||||||||| ||||||| || |||||||||||||| ||  ||||||||||||| ||  |
ataggatctccaatactgactgtcagttttgttgtaccacgaagcatttt-gtaattttgacattaccc-ttcatgacattttgcactgttgtgatggccagATGGCTGGGAAAGTCGGTGGGTCAAGTCCGAGTGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACCTCGGGAAAATGGAATGGAGATGCCGA

upper sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 1
-cgggtagtcctttttcggagttcatttgtattttctttaatcctagatcagtatttcccacttttctaactcgtgtgcatgtgctttgt-gtggatgccagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACGTGGCTGGGGAGTGGAACCACACCTCTGGTCAATGGAATGGAGACGCTAA
   ||   |||  |   |    ||| || | | | |    |  |    ||  || |    |  || | | ||        | |||  ||| |||   |||||| || ||||||| ||| ||||| || || || |||||||| || || ||| ||||||| || |||||||||||||| ||  ||||||||||||| ||  |
ataggatctccaatactgtctgtcagttttgtataccgcgaaacattttc--taatgtttatattaccatctgtgacatttctgcgctgttgtgatggccagATGGCTGGGAAAGTCGGTGGGTCAAGTCCGAGTGGAAAAAGGACGATAACATGGCTGGTGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGA

upper sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 3'ss of exon 1
cgggtagtcctttttcggagttcatttgtattttctttaatcctagatcagtatttcccacttttctaactcgtgtgcatgtgctt------tgtgtggatgccagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACGTGGCTGGGGAGTGGAACCACACCTCTGGTCAATGGAATGGAGACGCTAA
   ||| |   |||| |   ||||||  | ||  |||   |  |  |  | | ||||||  ||| |||| |  | || || || ||      ||  |       ||| || |||||  |||||||||||  ||| |||||||| |||||||||||| |||| ||| | |||||| |||| |||||  |||||| ||| ||| | ||
---gta-taactttttgtttttcattaatcttcacttcttttttcaa--attgtttccctttttactaagttttatgaatatgtttccataatggctaacatttagATGGATGGGAGGATCGATGGGTTGTATCTGATTGGAAGAAAGATGAGAACTTGGCAGGGCAATGGAACTACACTTCTGGGAAATGGAGTGGGGACCCGAA

upper sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 1
cgggtagtcctttttcggagttcatttgtattttctttaatcctagatcagtatttcccacttttctaactcgtgtgcatgtgctttgtgtggatgcca-gACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACGTGGCTGGGGAGTGGAACCACACCTCTGGTCAATGGAATGGAGACGCTAA
| | || ||| |  | |   |  |||  ||  |   |   | ||   | |  | || ||    ||    ||  | || |  |  ||| ||   |    | || || ||||| |||   ||||||||||| || ||||| |||||||||||| |||||||||| |||||| ||||||||||| ||||| |||||||| | ||
ctgataatccatgcttgtt-tcaattaataaatcagtatttgctttcttatgactttcctgcattgggtctaatatgtaattcatttttgaatactttaagATGGATGGGAGAATAAGTGGGTTAAATCCGAATGGAAGAAAGATGAGAACATGGCTGGGGAATGGAACTACACCTCTGGTAAATGGCATGGAGACCCGAA

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|18692974|gb|BM521822.1|BM521822
EST:     TGTCCATCGCTTCCGCCAATGTCTTCTTCGAAGAGCGTTTCGATG                         ACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACG
genomic: TGTCCATCGCTTCCGCCAATGTCTTCTTCGAAGAGCGTTTCGATGgtataaaatc ... tggatgccagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACG
EST: gi|193681359|gb|FK623249.1|FK623249
EST:     TCTCTTGTCCATCGCTTCCGCCAATGTCTTCTTCGAAGAGCGTTTCGATG                         ACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACG
genomic: TCTCTTGTCCATCGCTTCCGCCAATGTCTTCTTCGAAGAGCGTTTCGATGgtataaaatc ... tggatgccagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACG
EST: gi|208085877|gb|GD882453.1|GD882453
EST:     TGTCCATCGCTTCCGCCAATGTCTTCTTCGAAGAGCGTTTCGATG                         ACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACG
genomic: TGTCCATCGCTTCCGCCAATGTCTTCTTCGAAGAGCGTTTCGATGgtataaaatc ... tggatgccagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACG
EST: gi|192334620|gb|FK025195.1|FK025195
EST:     ACTCTTGTCCATCGCTTCCGCCAATGTCTTCTTCGAAGAGCGTTTCGATG                         ACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACG
genomic: TCTCTTGTCCATCGCTTCCGCCAATGTCTTCTTCGAAGAGCGTTTCGATGgtataaaatc ... tggatgccagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcagtatttcccacttttctaactcgtgtgcatgtgctttgtgtggatgccagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACGTGGCTGGGGAGTGGAACCACACCTCTGGTCAATGGAATGGAGACGCTAA
                  ttctaac  putative branch site (score: 1)
                ttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgggtagtcctttttcggagttcatttgtattttctttaatcctagatcagtatttcccacttttctaactcgtgtgcatgtgctttgtgtggatgccagACGGGTGGGAAAATCGATGGGTTAAATCAGATTGGAAAAAAGATGAGAACGTGGCTGGGGAGTGGAACCACACCTCTGGTCAATGGAATGGAGACGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA