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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattatctatttatcttgaactttgacaggcatgtctcatgattattttccctcacacagtgtttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

Basic information

species Glycine max
transcript GLYMA10G44150.1
intron # 46
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G44150.1 (Glycine max), 3'ss of exon 46
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 3'ss of exon 12
--------gtaagtattatctatttatcttgaactttgacaggcatgtctcatgatt--attttccctcacacagtgttttt-ttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
         |||| ||| | |   | | ||   ||  |  |   || | | |   |   ||| ||      | | |   | | | ||||| || || ||||||||||| ||||| ||||||||  | ||||||||||| ||||| ||||||||||||||||| |||||||| |||||||| ||||||
gtaagctgctaagcattctatgcatgtgttactctgcg-taattatatttgaaattcgaattatcaggattaaaatacctctctcagGGTCGTTGAGGATTTCAGAGACTGGACGAATTGGCTGTTTTACCGAGGTGGTATTGGGGTTAAGGGAGAAGAAAGTTGGGAAGCCTGGTGGGATGAAGAA

upper sequence: GLYMA10G44150.1 (Glycine max), 3'ss of exon 46
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 11
--------gtaagtatt------atctatttatcttgaactttgacaggcatgtctcatgattattttccctcacacagtgtttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
          ||| |||      |||||| ||   | |  |   |  | |||       |||||  || |   || |       | ||||| | || || ||||||||||| ||||||||||||||  | || |||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||
gtaagcagccaagcattttgtgtatctatgtactataagttcaaattgtcat--tatgagattagatttcaa-acccttctccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

upper sequence: GLYMA10G44150.1 (Glycine max), 3'ss of exon 46
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 45
gtaagta--------ttatctat-ttatcttgaactttgacaggcatgtctcatgattattttccctcacacagtgtttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
||||||         |||| ||| | || ||||   ||||    | ||| ||    | |    |  | | |   | |  ||| || || ||||| || |||| ||| ||||||||||||||  | ||| |||||||||||||||| || ||||  |||||||||||||| |||||||||||||||
gtaagtggtgctatcttatttatatcatgttgagtgttgagtaacgtgtttctcattgaacaacaataaaat--tatgctttcagAGTCGTGGAGGACTTCAAAGAATGGACAAATTGGCTCTTTTACAGAGGTGGAATTGGTGTGAAAGGAGCTGAAAGCTGGGAAGCATGGTGGGAAGAAGAA

upper sequence: GLYMA10G44150.1 (Glycine max), 3'ss of exon 46
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 43
gtaagtattatctatttatcttgaactttgacaggcatgtctcatgattattttccctcacacagtgttt-ttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
|||||||| || | | ||  ||   || | |  |   || |||||| ||  ||  ||        |     |||||||   ||||| || ||  | ||||||||||| |||||  | ||| ||||||||||||| |||||||||| |||||||||||| ||||||||||| ||||||
gtaagtatcatttttctaattttctctctcatggatttg-ctcatgttttattaaccatttgttttaccccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA

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|51335880|gb|CO979746.1|CO979746
EST:     GATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
genomic: GATTTGAGTGGCAAAAgtaagtatta ... gtttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGG
EST: gi|208248479|gb|GE047140.1|GE047140
EST:     TGGTTGTTTGCTCCATATTTATTCAACCCGTCTGGATTTGAGTGGCAAAA                         GGTGGTGGAAGATTTCAGAGATTGG
genomic: TGGTTGTTTGCTCCATATTTATTCAACCCGTCTGGATTTGAGTGGCAAAAgtaagtatta ... gtttttttagGGTGGTGGAAGATTTCAGAGATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaactttgacaggcatgtctcatgattattttccctcacacagtgtttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA
                                 ccctcac  putative branch site (score: 3)
                                            tgttttttt  putative PPT
                      atgattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattatctatttatcttgaactttgacaggcatgtctcatgattattttccctcacacagtgtttttttagGGTGGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG