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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttggaggaactaaaaacatatttaagcctaatatattaatgacattgcaatttactgttaaatatataaagtttaatgtattttattttctaaacagGCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGATAGTCAGGAAAGAAGCAAATTCGAG

Basic information

species Glycine max
transcript GLYMA14G07850.3
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G07850.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 12
aacttggaggaactaaaaacatatttaagcctaata---tattaatg-acattgcaatttactgttaaatatataaagtttaatgtattttattttctaaacagGCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGATAGTCAGGAAAGAAGCAAATTCGAG
       |     |   | | |   ||| |  | |    | |||||    ||| | || ||||    | |   | | |    || |  |||  ||   |  ||||||||| |||||||||| || ||||||||||||||||| |||||||| || || || |||  |  ||| | | ||
----caaaatgcttgtcagcctccctaaactcactggcctcttaatatgtattcccatgtacttgggatttatttatgacatatatgcttttcttctaatgcagGCTTTGCATGAAGCTTTAATGAGACAAGAAGAACTTCTTGCATACATAGACAGGCAAGAAGAAGCCAAGTCCCAG
















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|22525411|gb|BU084222.1|BU084222
EST:     TTATCGTGTGGACGCATTGGAAGCGGAACTGATCGCTACAAAGAAG                         GCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGAT
genomic: TTATCGTGTGGACGCATTGGAAGCGGAACTGATCGCTACAAAGAAGgtaactacat ... ttctaaacagGCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGAT
EST: gi|213594004|gb|DB983184.1|DB983184
EST:     GATCGCTACAAAGAAG                         GCTTGGTATGAAGCTTTGATTAGACAAGAAGAACTTTTGGCATACATTGAT
genomic: GATCGCTACAAAGAAGgtaactacat ... ttctaaacagGCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGAT
EST: gi|151401385|gb|EV271199.1|EV271199
EST:     CTGTTTATCGTGTGGACGCATTGGAAGCGGAACTGATCGCTACAAAGAAG                         GCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGAT
genomic: CTGTTTATCGTGTGGACGCATTGGAAGCGGAACTGATCGCTACAAAGAAGgtaactacat ... ttctaaacagGCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGAT
EST: gi|209700986|gb|BW664167.1|BW664167
EST:     CTGTTTATCGTGTGGACGCATTGGAAGCGGAACTGATCGCTACAAAGAAG                         GCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGAT
genomic: CTGTTTATCGTGTGGACGCATTGGAAGCGGAACTGATCGCTACAAAGAAGgtaactacat ... ttctaaacagGCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGAT
EST: gi|120532823|gb|EH260956.1|EH260956
EST:     CTGTTTATCGTGTGGACGCATTGGAAGCGGAACTGATCGCGACAAAGAAG                         GCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGAT
genomic: CTGTTTATCGTGTGGACGCATTGGAAGCGGAACTGATCGCTACAAAGAAGgtaactacat ... ttctaaacagGCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGAT
EST: gi|18848900|gb|BM568010.1|BM568010
EST:     CTGTTTATCGTGTGGACGCATTGGAAGCGGAACTGATCGCTACAAAGAAG                         GCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGAT
genomic: CTGTTTATCGTGTGGACGCATTGGAAGCGGAACTGATCGCTACAAAGAAGgtaactacat ... ttctaaacagGCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgcaatttactgttaaatatataaagtttaatgtattttattttctaaacagGCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGATAGTCAGGAAAGAAGCAAATTCGAG
                            gtttaat  putative branch site (score: 4)
                                      ttttattttct  putative PPT
      aatttactgttaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttggaggaactaaaaacatatttaagcctaatatattaatgacattgcaatttactgttaaatatataaagtttaatgtattttattttctaaacagGCTTTGTATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATTGATAGTCAGGAAAGAAGCAAATTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA