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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaatgcaaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtagatgtattatggtctaagcacttgattatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG

Basic information

species Glycine max
transcript GLYMA11G15020.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 7
cttaatgcaaggttaacttttttgaagcaaaga-attttttcaatacaatatttatgtagatgtat-tatggtctaagcacttgattatatat-ctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG
          |     || || |    |||| | | |   |  || | ||||||   ||      |  |  ||  |   |||||| |  || | ||| | |||||||  | ||||||||||| ||||| || ||||| || |||||  |||||||||| ||||| ||||||||||| || |
----------gtacgtctgttctatcacaaatacactacatttatcctatattttcttaatctagtgcaaagttcacttacttgaattgatttacttcatcagGAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
cttaatgcaaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtagatgtatt----atggtctaagcacttgatta---tatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG
      | ||  ||   |  | ||||      ||||| ||   |    | |||    |  | | ||     |  ||| |    || |||    | | | | || |||| ||| | ||||| ||||||||||| || ||||| ||||| || ||||||||||| ||||| | ||||||||| || |
------gtaaatttg-ttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG

upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 8
--------cttaatgc-aaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtagatgtattatggtctaagcacttgattatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG
        ||| ||   ||  || |  ||| |        |    ||||  ||| | ||| | |  || | | |||  || |    | || | | | | ||| |  |||| ||| | ||||| ||||||||||| || ||||| || || |  ||||||||||| ||||| ||||||||||| || |
gtaaatttcttcatctgaaaattgaaatttatttgctttgg----tttttcataaattatctttcaagttctcttacagtttt--tatttaactttttttctat--cagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 7
cttaatgcaaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtag-atgtattatggtcta----agcacttgatta--tatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG
      | ||  ||     | |  ||    | | || |||   |    | || ||  |  || | | | | |||     ||   ||  |||  | | | | || |||| ||| | ||||| ||||||||||| || ||||| || || |  ||||||||||| ||||| ||||||||||| || |
------gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagtttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
---cttaatgcaaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtagatgtattatggtctaagcacttgattatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG
     |  | |     |  || |||| ||    |  |  | |    |  |  | |||||   || ||  |   ||   | |  |  |   |  |   | ||||| || || || ||||||||||||||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||||
aatactgttactcttctttctcttttaaaattgaagacatgtc---ttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG

upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------cttaatgcaaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtagatgtattatggtctaagcacttgattatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG
                       |||  ||||   | |   | | || ||      |  | |   |||||  ||   | || |   | |||   || | |  ||| || | | ||||    ||||||  | || |||||||| ||||| || ||||| ||||| ||| | |||||||| || ||||||||||||||  | |
gtaaatccaactcacgttacacgcttggtgcaccatcacgctctgtgcagtttctgaactct--gatacacaatcattctacacaaaatattaccttaacg-ttgcttct-tgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG

upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ17446 (Selaginella moellendorffii), 3'ss of exon 6
cttaatgcaaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtagatgtattatggtctaagcacttgattatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG
                                           |||       |  ||  ||| ||   |||||    | || | || | |    | |||| ||| | || ||||| || ||||| ||||| ||||| ||||| ||||||||||| ||||| |||||||| || || |
------------------------------------------gtacgtgcaccagatatttgtctt---gtctac-tgcctgctcat-tgtgccgagcagGTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG

upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ35029 (Selaginella moellendorffii), 3'ss of exon 6
cttaatgcaaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtagatgtattatggtctaagcacttgattatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG
                                           |||       |  ||  ||| ||   |||||    | || | || | | |  | |||| ||| | || ||||| || ||||| ||||| ||||| ||||| ||||||||||| ||||| |||||||| || || |
------------------------------------------gtacgtgcaccagatatttgtctt---gtctac-tgcctgctcat-tgtgtcaagcagGTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG

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|7233416|gb|AW568762.1|AW568762
EST:     TCTTGTGCATCCCCAACCTGAAGGCTATTGGGGCAATGTGAACCCTATTG                         GAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGT
genomic: TCTTGTGCATCCCCAACCTGAAGGCTATTGGGGCAATGTGAACCCTATTGgtacatgctt ... tctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGT
EST: gi|17022039|gb|BM093073.1|BM093073
EST:     TCTTGTGCATCCCCAACCTGAAGGCTATTGGGGCAATGTGAACCCTATTG                         GAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGT
genomic: TCTTGTGCATCCCCAACCTGAAGGCTATTGGGGCAATGTGAACCCTATTGgtacatgctt ... tctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGT
EST: gi|192301457|gb|FG994081.1|FG994081
EST:     TCTTGTGCATCCCCAACCTGAAGGCTATTGGGGCAATGTGAACCCTATTG                         GAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGT
genomic: TCTTGTGCATCCCCAACCTGAAGGCTATTGGGGCAATGTGAACCCTATTGgtacatgctt ... tctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatatttatgtagatgtattatggtctaagcacttgattatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG
                                acttgat  putative branch site (score: 5)
                                           tatcttt  putative PPT
                                  ttgattatatatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaatgcaaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtagatgtattatggtctaagcacttgattatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - -tgcaagg
- - - - - - - - - - - -gaagcaaa
- - - - - - - - - - - - - - - - - - - - caataca
- - - - - - - - - - - - - - - - - - - - - - - - - - tatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaagca