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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttgtaaatttgtttcctagtacctttattaagatgagtgtagttgatttttcaatattctattattgaatggtgtggttctgatgtggcatatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAGAGTGAAGAACTGGATTACTATTAATGAGCCCCTTCAAACTGCAGTCAAT

Basic information

species Glycine max
transcript GLYMA11G16220.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G16220.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g67220.1 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------ccttgtaa--atttgtttcctagtacctttattaagatgagtg---tagtt----gatttttcaatattctattattgaatggtgtggttctga-tgt-ggcatatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAGAGTGAAGAACTGGATTACTATTAATGAGCCCCTTCAAACTGCAGTCAAT
                                                        || | |||  | ||  |      ||   |||||||||||||||   |||||    |   || |||  ||   ||  |  ||| || | |||| | |||    |||| |||| |||||||||||  | ||||||||  |||||||||||| |||||| || ||||| ||| | ||||| || || |||||||| |||||||||||||| |||
gtaagacactacgacatctttactttgcactatgatttaaaaagtcatttaaacagccatataaccaatttataagggatattattattaagatgagtgatttagtttaaagtgcttgcaaacttgatttggtttatg-tgagtttcttactgtcaaaatatcccagGGAGTACTTTGCACTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGAGTAAAGCATTGGATAACAATCAATGAGCCTCTTCAAACTGCAGTTAAT

upper sequence: GLYMA11G16220.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G044092_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------------ccttgtaaatttgtttcctagtacctttattaagatgagtgtagttgatttttcaatattctattattga-atggtgtggttctgatgtggcatatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAGAGTGAAGAACTGGATTACTATTAATGAGCCCCTTCAAACTGCAGTCAAT
                                                                        | | | |  || ||| | || ||  || || |       || ||||    ||  || |||| |  || | |||   |  |    ||    ||||| |||| |||||||||||  | ||||||||  |||||||||||| |||||| || || || ||| | ||||| || || ||||| || || ||||||||| |||||
gtaagtcactgcaggcatctttagtgtgcagtatgattaccaaagttttcttgacgcttaaacggatgattacatatgagattcttttcgag-acaattttttatccagaagtggttgcaactt-gattttctgtagtttatatgagtttctcaccataaaacatatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGGGTAAAGCATTGGATAACGATCAATGAACCTCTCCAAACTGCAATCAAT

upper sequence: GLYMA11G16220.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G36890.1 (Arabidopsis thaliana), 3'ss of exon 6
ccttgtaaatttgtttcc-tagtacctttattaagatgagtgtagttgatttttcaatattc-tattattgaatggtgtggttctgatgtggcatatgc---cagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAGAGTGAAGAACTGGATTACTATTAATGAGCCCCTTCAAACTGCAGTCAAT
    |     |  | ||  |    |||||    || || |  ||    ||    || | ||| ||  ||| |||  | ||    | |  |    |   |   ||| || || ||||   | ||||||||| |||| ||||| | |||||| |||||||||||| ||||||| ||  | ||||| || ||||| ||  | || |||
----gagggctaatatctatgaagcctttccctagctg-gaataaacaatgcagcacttttcatagaatttaataatttgacattaaacttttcttcacgtgcagCGATTATTTTGGCCTCTATGCAGATGCTTGTTTTGCCAATTTTGGTGATAGAGTGAAGCACTGGATCACATTAAATGAACCTCTTCAGACCTCGGTGAAT

upper sequence: GLYMA11G16220.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0220g00070.t01 (Vitis vinifera), 3'ss of exon 5
ccttgtaaatttgtttcctagtaccttta--ttaagatgagtgtagttgatttttcaatattctattattgaatggtgtggttctgatgtggcatatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAGAGTGAAGAACTGGATTACTATTAATGAGCCCCTTCAAACTGCAGTCAAT
  || |||| ||  |   |  ||     |   | | ||    || |  |  |     ||  |  ||   | |||| |  |  | |  ||    | ||  |||| | || |||||  ||||||| || |||||||||||||||||||| |||||||| ||||||||||| ||  | |||||||| ||||||||||| || |||
--ttttaaaatttatctttgctattccaaacctcacatactggttgaaggatccattattgttcatacataaatgtttggtatattttggtaaacattgcagAAAATATTTTGCAATTTATGCGGAAACTTGCTTTGCAAGTTTTGGTGATAGAGTAAAGAACTGGATCACATTAAATGAGCCTCTTCAAACTGCGGTGAAT

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|298170350|gb|HO018974.1|HO018974
EST:     CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTGAATAAACAAATCAT                         AGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
genomic: CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCATgtaggtatca ... catatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
EST: gi|151395074|gb|EV264945.1|EV264945
EST:     CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT                         AGAGTACTTTGCTGTTTATGCAGATACCTGCTTTGCAAGTTTTGGGGATAG
genomic: CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCATgtaggtatca ... catatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
EST: gi|151393509|gb|EV263384.1|EV263384
EST:     CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT                         AGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
genomic: CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCATgtaggtatca ... catatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
EST: gi|192300022|gb|FG991840.1|FG991840
EST:     CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT                         AGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
genomic: CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCATgtaggtatca ... catatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
EST: gi|254323234|gb|GR840039.1|GR840039
EST:     CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT                         AGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
genomic: CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCATgtaggtatca ... catatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
EST: gi|192296626|gb|FG991194.1|FG991194
EST:     CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT                         AGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGGATA
genomic: CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCATgtaggtatca ... catatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGG-ATA
EST: gi|26268409|gb|CA819472.1|CA819472
EST:     CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT                         AGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
genomic: CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCATgtaggtatca ... catatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
EST: gi|192314382|gb|FK008058.1|FK008058
EST:     CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT                         AGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
genomic: CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCATgtaggtatca ... catatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
EST: gi|192314383|gb|FK008059.1|FK008059
EST:     CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT                         AGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG
genomic: CCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCATgtaggtatca ... catatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttttcaatattctattattgaatggtgtggttctgatgtggcatatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAGAGTGAAGAACTGGATTACTATTAATGAGCCCCTTCAAACTGCAGTCAAT
                                  ttctgat  putative branch site (score: 3)
     tttcaatattctatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttgtaaatttgtttcctagtacctttattaagatgagtgtagttgatttttcaatattctattattgaatggtgtggttctgatgtggcatatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAGAGTGAAGAACTGGATTACTATTAATGAGCCCCTTCAAACTGCAGTCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
ccttgta
- - - - - -tgtttcc
- - - - - - - - - - gtacctt
- - - - - - - - - - - - - - - - - -tgagtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgtgg