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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaaattaatttgtttctcatctcatcccttttgcctcctttgagatttgattttgttttattgattcttagcttcttctgtgttgccaaactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACC

Basic information

species Glycine max
transcript GLYMA10G44210.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g33860.1 (Oryza sativa), 3'ss of exon 5
tttaaattaatttgtttctcatctcatcccttttgcctcctttgagatt-tgattttgttttattgattct-tagcttcttctgtgttgccaaactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACC
   | |  |||   | | | |     |    ||  | |  ||||  |   || || |   | ||| | ||  |    | | || ||||  ||  |  | ||| ||||| |||||||| ||||||||||| ||||||||||| ||||||||||| || |||||||| |||||||| || || || ||||| || || || || 
--aagaccaatagttctatgaataactgaagttcccattatttgttaccatgcttgttaatcattcactcagtcatgtatcctttgttctcactccatgcagGTATGCCATGACTGGCCAGTTGACTCAGAAAAGTGATGTATATAGTTTTGGAGTTGTTCTTCTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCACACA

upper sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g62700.1 (Oryza sativa), 3'ss of exon 5
tttaaattaatttgt-ttctcatctcatcccttttgcctcctttgagatttgattttgttttat-tgattcttagcttcttctgtgttgccaaactt--tacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACC
   |||| |   |   |  || |  |||   || ||       |  |||    | |  ||||||    ||| |  |||    | | |  ||  ||||    ||||||||| |||||||| ||| |||| || || |||||||| || ||||||||||| |||||| | || || || ||||| || ||||| || ||||| || 
---aaatgaggataagtgttcttggcatgagttgtggaaatactt-gatgccgtgtatttttatgcatttcctctcttaacttatataaccctacttgccgcagATATGCTATGACTGGCCAGCTGACGCAGAAGAGTGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACA

upper sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G153945_T03 (Zea mays), 3'ss of exon 5
tttaaattaatttgtttctcatctcatcccttttgcctcctttgagatttgat-tttgttttattgattcttagcttcttctgtg--ttgccaaactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACC
  |||  |||| | ||    || |    |    ||  |  ||||  | || || ||||||       |  | ||   | |  | |   |   | || || ||| ||||| |||||||| ||  ||||||||||||||||||| ||||||||||| || || ||| | |||||||||||||| || |||||||| || ||||| 
-ctaa--taatcttttcactattttgcacgagatgaatgttttggaactttatctttgttcctcatctgatcagtgacataagagatctattatacatttcagGTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGGGGTTGTCCTTTTAGAGCTTCTTACTGGAAGGAAACCTGTAGATCATACA

upper sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G001668_T01 (Zea mays), 3'ss of exon 5
-----tttaaattaatttgtttctcatctcatcccttttgc---ctcctttgagatttgattttgttttattgattcttagcttcttctgtgttgccaaactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACC
      | ||| || ||| ||| |    | |||  |         |  ||  || | || |||| |||      |||| |  ||       |  || |     ||||| ||||| |||||||| ||| |||| ||||||||||||||||| || ||||||||||||||| | || ||| | ||||| || ||||| || || || || 
ttgtactgaaaatagtttttttat-gcatgatctgtagaaaaaaatatttgaagctctggttttctttccgcctttctgaattt-------ggagctacttggtacagGTATGCTATGACTGGCCAGCTGACACAAAAAAGTGATGTCTACAGCTTTGGTGTGGTTCTTTTGGAACTTTTGACTGGAAGGAAACCAGTAGATCACACA

upper sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
tttaaattaatttgtttctca-tctcatcccttttgcc--tcctttgagatttgattttgtttt-attgattcttagcttcttctgtgttgccaaactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACC
   ||| | ||| ||| ||   | |||    | | |    |  | |   |  | | |   |  | | ||||||  |  ||  | |||||        | |  || |||||||||||||| || |||||||| || |||||||| ||||||||||| || |||||  | |||||||| ||||| |||||||||||||| ||||||
---aaaattattagttgcttgctttcaattgtctaggaagtattatagtaaattactaaatcctgactgattcaca-tttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC

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|7692618|gb|AW760720.1|AW760720
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
EST: gi|11273675|gb|BF324133.1|BF324133
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
EST: gi|27424278|gb|CA935798.1|CA935798
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
EST: gi|11273885|gb|BF324274.1|BF324274
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
EST: gi|298178999|gb|HO024734.1|HO024734
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
EST: gi|8826662|gb|BE210392.1|BE210392
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
EST: gi|6566081|gb|AW233841.1|AW233841
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
EST: gi|15204621|gb|BI427389.1|BI427389
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTT
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTT
EST: gi|17022632|gb|BM093666.1|BM093666
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
EST: gi|11688386|gb|BF596062.1|BF596062
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
EST: gi|23727138|gb|BU761587.1|BU761587
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
EST: gi|151406097|gb|EV275912.1|EV275912
EST:     CGCCTTCATTCA-CTCGTGTATTGGGAACTTTTGG-TATCATGCTCCAGA                         -TATGCA-TGACTGGGCAGTTGAC
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGAC
EST: gi|192327312|gb|FK019559.1|FK019559
EST:     CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGA                         ATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG
genomic: CGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttg ... aactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttgattttgttttattgattcttagcttcttctgtgttgccaaactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACC
               tattgat  putative branch site (score: 3)
      attttgttttattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaaattaatttgtttctcatctcatcccttttgcctcctttgagatttgattttgttttattgattcttagcttcttctgtgttgccaaactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - -tcatccc
- - - - - - - - - - - - - - - - - -cctcctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgcc