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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactatataaacctttttgtgggggagaatgttgttaaaataatgacatgactctgccatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG

Basic information

species Glycine max
transcript GLYMA20G16170.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g58020.3 (Oryza sativa), 3'ss of exon 12
tactatataaacctttttgtgggggagaatgttgttaaa--ataatgac----atgactctgccatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG-----
     |||    ||||   |     |   |  |   |||  || ||  |    ||  ||   | |||    || | | | |     | |||  ||  |  || |||||||||| || |||||||||||||| || |||||||||||  ||||  |||| ||||||||||| | ||| ||||| || ||||| ||| | |||     
----gtatgttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatctgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGGTTCT

upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 12
tactatataaacctttttgtgggggagaatgttgttaa--aataatgac----atgactctgccatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG
     |||    ||||   |     |   |  |   ||  ||| ||  |    ||  ||   | |||    || | | | |     | |||  ||  |  || |||||||||| || |||||||||||||| || |||||||||||  ||||  |||| ||||||||||| | ||| ||||| || ||||| ||| | |||
----gtatgttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatctgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG

upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 12
-tactatataaacctt--tttgtgggggagaatgttgtt--aaaataatgacatgactctg---ccatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG
 ||  || |   | ||  |           | | ||  |  | | ||||| |  |  | ||       | |  ||   | || ||     |        ||||| |||||||||| || ||||| ||||||||||| |||||||| ||  ||||| |||||||||| ||||| | |||||| || || || || ||| | |||
gtatgatttcttctttgttccactcattgtagtcttactgcatattaatgtctggtttttgaagttgcagttcttccatttttaaatccctcattgtcttgttt-cagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG

upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 12
--------------------------------------------------------------------------------tactatataaacctttttgtgggggagaatgttg---ttaaaataatgacatgactctgccatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG
                                                                                    | |  ||        |    ||  |||| |   ||||| |  |||  |    |    |  ||     | | |  | |||| | || || |  ||||||||||| ||||||||||||||||| || ||||| ||||| ||  | ||| |||| ||||| || || || ||||| || || |||||||||||||||
gtaagaaggctccccccctctcccttgattatgagatcacacagatgatacatgtttataaaccttcatctatcatatgtggaaacaacaagtgcagcatcaaagaacatgtagaacttaaacttttgatgttctccccagaattttaacctctatatatggttttctcgtcga--tttgcagTGGTGGGACCCAATGGTATTGGTAAATCAACAATACTCAAACTTATTTCTGGCGATCTGCAACCAAGCTCTGGAACAGTTTTCCGTTCTGCTAAG

upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 12
tactatataaacctttttgtgggggaga-atgttgttaaaataatgacatgactctgccatattgtttatgtgttgaaggttatttcctcaatgttt-gcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG
   | | | | | ||||  | ||   || |     || |  |  |   ||   | | || |||  | | | |    |     || |||  | ||||| ||||||||||| || ||||| ||||| || ||||||||||| || || ||||| ||||| ||||| || || ||||| || || |||||||| || |||
--gtcttttagcattttattaggcatgatactgcatttatttggttttattgtttttccctatcttatttttccaaatctggatctccaaattgttttgcagTGGTTGGGCCAAATGGCATTGGTAAATCAACTATACTCAAATTGATTGCAGGGGAACTTCAACCAAGCTCTGGAACGGTATTCCGTTCGGCCAAG

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|13789096|gb|BG651687.1|BG651687
EST:     TCTTTTTAAGAATTTGAACTTTGGGATTGATCTCGACAGTCGAATTGCAA                         TGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTG
genomic: TCTTTTTAAGAATTTGAACTTTGGGATTGATCTCGACAGTCGAATTGCAAgtaagaatat ... atgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTG
EST: gi|22523787|gb|BU082598.1|BU082598
EST:     TCTTTTTAAGAATTTGAACTTTGGGATTGATCTCGACAGTCGAATTGCAA                         TGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTG
genomic: TCTTTTTAAGAATTTGAACTTTGGGATTGATCTCGACAGTCGAATTGCAAgtaagaatat ... atgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTG
EST: gi|192322574|gb|FK014695.1|FK014695
EST:     TCTTTTTAAGAATTTGAACTTTGGGATTGATCTCGACAGTCGAATTGCAG                         TGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTG
genomic: TCTTTTTAAGAATTTGAACTTTGGGATTGATCTCGACAGTCGAATTGCAAgtaagaatat ... atgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTG
EST: gi|207843169|gb|GD815119.1|GD815119
EST:     TCTTTTTAAGAATTTGAACTTTGGGATTGATCTCGACAGTCGAATTGCAA                         TGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTG
genomic: TCTTTTTAAGAATTTGAACTTTGGGATTGATCTCGACAGTCGAATTGCAAgtaagaatat ... atgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgactctgccatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG
             atattgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactatataaacctttttgtgggggagaatgttgttaaaataatgacatgactctgccatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG

- - - - - - - - - gtggggg
- - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - -tgacatg
- - - - - - - - - - - - - - - - - - - - - - - - - -ctctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa