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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgactactattatacttatgttcctttctcttaaaacgttgaaatcaattgtagattatagtgtcaaacagttttcttagctatgtctttcttgtttcagGTATATGCTGAAGGACCTGCTCGTCCCACTGGAGGAGCTGCTGCAATTGCCATGCTTGTAGGGCCAGATGCTCCTATTGCTTTTGAAAGCAAACTCAGAG

Basic information

species Glycine max
transcript GLYMA16G32480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0036g00810.t01 (Vitis vinifera), 3'ss of exon 3
tgactactattatacttatgttcctttctcttaaaacgttgaaatcaattgtagattatagtgtcaaacagtt---ttcttagctatgtctttcttgtttcagGTATATGCTGAAGGACCTGCTCGTCCCACTGGAGGAGCTGCTGCAATTGCCATGCTTGTAGGGCCAGATGCTCCTATTGCTTTTGAAAGCAAACTCAGAG
    || | ||||   |   |     | | |  | |  |  |  |   |  |   |||||   |   |  |||   ||| |  ||     |||| | | |||||| ||||| |||| ||  ||| | || ||| ||||||| ||||| ||||| ||||| |||||||| |||||||||||| | |||||||||||| | || |
---ttagtcttatttgtgcatcaaaatatatctagatttaaatcttcttcatgtgttataagctagcaatgttctattccttactggaggtttcctttatcagGTTTATGCAGAAGAACTAGCTAGGCCTACTAGAGGAGCAGCTGCTATTGCTATGCTAGTAGGGCCTGATGCTCCTATTACATTTGAAAGCAAATTGAGGG

upper sequence: GLYMA16G32480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g04580.t01 (Vitis vinifera), 3'ss of exon 4
tgactactattatacttatgttcctttctcttaaaacgttgaaatcaattgtagattatagtgtcaaacagtt---ttcttagctatgtctttcttgtttcagGTATATGCTGAAGGACCTGCTCGTCCCACTGGAGGAGCTGCTGCAATTGCCATGCTTGTAGGGCCAGATGCTCCTATTGCTTTTGAAAGCAAACTCAGAG
    || | ||||   |   |     | | |  | |  |  |  |   |  |   |||||   |   |  |||   ||| |  ||     |||| | | |||||| ||||| |||||||| ||| | || ||||||||||| ||||| ||||| ||||| |||||||| |||||||||||||| |||||||||||| | || |
---ttagtcttatttatgcatcaaaatatatctagatttaaatcttcttcatgtgttataagctagcaatgttctattccttactggaggtttcctttatcagGTTTATGCAGAAGGACCAGCTAGGCCTACTGGAGGAGCAGCTGCTATTGCTATGCTAGTAGGGCCTGATGCTCCTATTGCATTTGAAAGCAAATTGAGGG

upper sequence: GLYMA16G32480.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ12678 (Selaginella moellendorffii), 3'ss of exon 4
tgactactattatacttatgttcctttctcttaaaacgttgaaatcaattgtagattatagtgtcaaacagttttcttagctatgtctttcttgtttcagGTATATGCTGAAGGACCTGCTCGTCCCACTGGAGGAGCTGCTGCAATTGCCATGCTTGTAGGGCCAGATGCTCCTATTGCTTTTGAAAGCAAACTCAGAG
                                            | | || | ||| || | |  |||| | |  | |    |||||       || ||||| |||||||||||  ||||||||||||  || || |||| |||| |||||||||||||||| ||  | || ||  ||| | ||||  | |     |  |
-------------------------------------------gtaagttttcgatcatggagctaaaccggtgacctg--catgtca-----attgcagGTTTATGCTGAAGGCGCTGCTCGTCCCAGCGGCGGTGCTGGTGCAGTTGCCATGCTTGTAGGACCGAACGCGCCGCTTGTTCTTGATCGAAGCTATACCG

upper sequence: GLYMA16G32480.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ13836 (Selaginella moellendorffii), 3'ss of exon 4
tgactactattatacttatgttcctttctcttaaaacgttgaaatcaattgtagattatagtgtcaaacagttttcttagctatgtctttcttgtttcagGTATATGCTGAAGGACCTGCTCGTCCCACTGGAGGAGCTGCTGCAATTGCCATGCTTGTAGGGCCAGATGCTCCTATTGCTTTTGAAAGCAAACTCAGAG
                                            | | || | ||| || | |  |||| | |  |  ||| | |||       || ||||| |||||||||||  ||||||||||||  || || |||| |||  |||||||||||||||| ||  | || ||  ||| | | ||| | |     |  |
-------------------------------------------gtaagttttcgatcatggagctaaaccggtgacc-agc-acgtca-----attgcagGTTTATGCTGAAGGCACTGCTCGTCCCAGCGGCGGTGCTGGTGCGGTTGCCATGCTTGTAGGACCGAACGCGCCGCTTGTTCTCGAACGAAGCTATACCG

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|192294282|gb|FG986371.1|FG986371
EST:     GTAGCTCATGGGATGGACGTTATGGACTTGTTGTTTGTACAGACACTGCG                         GTATATGCTGAAGGACCTGCTCGTCCCACTGGAGGAGCTGCTGCAATTGCC
genomic: GTAGCTCATGGGATGGACGTTATGGACTTGTTGTTTGTACAGACACTGCGgtatgtctgc ... cttgtttcagGTATATGCTGAAGGACCTGCTCGTCCCACTGGAGGAGCTGCTGCAATTGCC
EST: gi|192293854|gb|FG986063.1|FG986063
EST:     GTAGCTCATGGGATGGACGTTATGGACTTGTTGTTTGTACAGACACTGCG                         GTATATGCTGAAGGACCTGCTCGTCCCACTGGAGGAGCTGCTGCAATTGCC
genomic: GTAGCTCATGGGATGGACGTTATGGACTTGTTGTTTGTACAGACACTGCGgtatgtctgc ... cttgtttcagGTATATGCTGAAGGACCTGCTCGTCCCACTGGAGGAGCTGCTGCAATTGCC
EST: gi|19052496|gb|BM731163.1|BM731163
EST:     GTAGCTCATGGGATGGACGTTATGGACTTGTTGTTTGTACAGACACTGCG                         GTATATGCTGAAGGACCTGCTCGTCCCACT
genomic: GTAGCTCATGGGATGGACGTTATGGACTTGTTGTTTGTACAGACACTGCGgtatgtctgc ... cttgtttcagGTATATGCTGAAGGACCTGCTCGTCCCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattgtagattatagtgtcaaacagttttcttagctatgtctttcttgtttcagGTATATGCTGAAGGACCTGCTCGTCCCACTGGAGGAGCTGCTGCAATTGCCATGCTTGTAGGGCCAGATGCTCCTATTGCTTTTGAAAGCAAACTCAGAG
                                      tgtctttcttgtttc  CT-rich tract
      tagattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgactactattatacttatgttcctttctcttaaaacgttgaaatcaattgtagattatagtgtcaaacagttttcttagctatgtctttcttgtttcagGTATATGCTGAAGGACCTGCTCGTCCCACTGGAGGAGCTGCTGCAATTGCCATGCTTGTAGGGCCAGATGCTCCTATTGCTTTTGAAAGCAAACTCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA