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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttggtgctgcattcttttgatgcctacttcctgatgatttttgtgtgctgatcataaattttttgttgtcttatgatggtttctgtttgtccttgaagGTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAAATCTTGCCGAGTGGATTCCA

Basic information

species Glycine max
transcript GLYMA06G15330.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g63430.1 (Oryza sativa), 3'ss of exon 6
ccttggtgctgcattcttttgatgcctacttcctgatgatttttgtgtgct--gatcataaattttttgttgtct-tatg-------atggtttctgtttgtccttga--agGTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAAATCTTGCCGAGTGGATTCCA
              | |||  || |   ||  |||||  || |    ||||  ||  ||| |||||||  | | | | ||       ||| ||||||||||||  |    || ||||| || || || |||||||| || ||||| ||||||||||||||| | || ||||| ||||||||  | |||||  |||   |  ||||||| || 
-----------tgctgtttgaattctcgctaactgatt-ttataacctgctaagagtatatatttttttctatatatgtggtgaaacatgatttctgtttgtctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCG

upper sequence: GLYMA06G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 6
ccttggtgctgcattcttttg-at----gcctacttcctgatgatttttgtgtgctgatcataaattttttgttgtcttatgatggtttctgtttgtccttgaagGTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAAATCTTGCCGAGTGGATTCCA
| |||   ||    | | ||| ||    |||||  |   |    | ||| | |  |  | |||      | | |||| | || |  || ||  ||||    | |||||| | ||||| |  |||||||| ||||||||||| ||| |||| ||||| |||||||| || |||||||||| |||| |||  ||  ||||||| || 
ctttgcatctaagatttgttgcataatggcctatattgagtccttgtttatatttttgttatac-caaatagatgtcatttggtttttcctacttgt----gtagGTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGCGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCG
















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|22522334|gb|BU081145.1|BU081145
EST:     CCAGAGTTGAAGCGGATCTACTATGAACTAATGATTCG                         GTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: CCAGAGTTGAAGCGGATCTACTATGAACTAATGATTCGgtaactgatt ... gtccttgaagGTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|26048081|gb|CA784677.1|CA784677
EST:     ATTCCATCTCTACCAGAGTTGAAGCGGATCTACTATGAACTAATGATTCG                         GTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCG
genomic: ATTCCATCTCTACCAGAGTTGAAGCGGATCTACTATGAACTAATGATTCGgtaactgatt ... gtccttgaagGTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCG
EST: gi|26048108|gb|CA784697.1|CA784697
EST:     ATTCCATCTCTACCAGAGTTGAAGCGGATCTACTATGAACTAATGATTCG                         GTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATTCCATCTCTACCAGAGTTGAAGCGGATCTACTATGAACTAATGATTCGgtaactgatt ... gtccttgaagGTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgctgatcataaattttttgttgtcttatgatggtttctgtttgtccttgaagGTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAAATCTTGCCGAGTGGATTCCA
  tgctgat  putative branch site (score: 3)
                                    tttctgtttgtcctt  putative PPT
          ataaattttttgttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttggtgctgcattcttttgatgcctacttcctgatgatttttgtgtgctgatcataaattttttgttgtcttatgatggtttctgtttgtccttgaagGTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAAATCTTGCCGAGTGGATTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- -tggtgct
- - - - - gcattct
- - - - - - - - - -tgatgcc
- - - - - - - - - - - - - - - -cctgatg
- - - - - - - - - - - - - - - - - - - - ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - -tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttctg