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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaactttggatacaataagaaccaaaatatttcccttgtcatttcttctgcatacttttcatgtgctatgctaccttaatgttgttcctgaatttccagGATATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGAGAAAAGATTTTTATGCAGTATCGAAATGAAATTCCATATGCATGTCAG

Basic information

species Glycine max
transcript GLYMA16G24870.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G24870.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g49220.2 (Oryza sativa), 3'ss of exon 5
gcaactttggata--caataagaaccaaaatatttccctt--gtcatttcttctgcatacttttc-atgtgctatgc-taccttaatgttgttcctgaatttccagGATATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGAGAAAAGATTTTTATGCAGTATCGAAATGAAATTCCATATGCATGTCAG
   |||   ||||  || |     |    || |||  ||   | || |   |    |||||     || |   ||   |   || ||||  |||  |   |||||||| || |  |||||||| || |||||||||||||| |  ||||| || ||||||||||||||| | ||||||||  | |||||||||||||| ||||||
---actcacgatatccagtgcttgctttgatgtttaactgcagccaataaatactgatactacaagatatcaaatatatttgttcatgtgattctcg---ttccagGACATAGCTAGTGAGCACCCTGAGAGATTTTTTGTGGGGGAAATAGTGAGAGAAAAGATTTTTCTTCAGTATCGTCAAGAAATTCCATATGCTTGTCAG

upper sequence: GLYMA16G24870.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G66470.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------gcaactttggatacaataagaaccaaaa---tatttcccttgtcatttcttctgcatacttttcatgtgctatgctac-----cttaatgtt-----gttcctgaatttccagGATATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGAGAAAAGATTTTTATGCAGTATCGAAATGAAATTCCATATGCATGTCAG
                                       |     | | || |   | | |  | |   || ||  |||   ||| ||   |  |    ||||  ||| |   | |     | ||||||      | |  |  ||||| |||||||||| || |||||||||||||||||||||||  |||| ||||||||||| || || ||||||||||| ||||||||| |||| ||||||||||||
gtactatgcatgaaaattccctgcttcagtattgaattcctctccttgctatagctaaagcttatagtctaatttgcttaatatt-ctgaggtttgtgcttcagatgcaacaattcacttacctaatgtcttacggctatttgatttctagGATATTGTGAGCGAGCATCCAGAGAGATTTTTTGTTTCTGAGATTGTTAGAGAGAAAATATTTATGCAGTACCGAAATGAAGTTCCTTATGCATGTCAG

upper sequence: GLYMA16G24870.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g02120.t01 (Vitis vinifera), 3'ss of exon 5
gcaactttggatacaataagaaccaaaatatttcccttgtcatttctt--ctgcatactttt--------catgtgctatgctaccttaatgttgttcc---tgaatttccagGATATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGAGAAAAGATTTTTATGCAGTATCGAAATGAAATTCCATATGCATGTCAG
              |  ||||| ||   | |||   |  || |||| |  ||| | ||| ||        ||| |      | | |  | ||||||| |   ||  |    |||| ||||| |||||||| || || ||||| ||||||| ||| ||||||||||||||||| || ||||| ||||| |||||| |||| ||||||||||||
-------------aacaaagaaacatgttttttttttaatcgtttcatgtctgaaaactattgcttgttgcatataactaacaatcacactgttgtttcacttgtttccttagGACATTGTTAGTGAGCACCCGGAAAGATTCTTTGTAGGTGAGATTGTTAGAGAAAAGATCTTCATGCAATATCGTAATGAAGTTCCTTATGCATGTCAG

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|58018987|gb|CX705729.1|CX705729
EST:     AGGACTGGATACTGTCAAAGCTTCCCAATGGACCAGCTTATTATCCAAAG                         GATATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGA
genomic: AGGACTGGATACTGTCAAAGCTTCCCAATGGACCAGCTTATTATCCAAAGgcatgtcaag ... gaatttccagGATATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGA
EST: gi|58019195|gb|CX705937.1|CX705937
EST:     AGGACTGGATACTGTCAAAGCTTCCCAATGGACCAGCTTATTATCCAAAG                         GATATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGA
genomic: AGGACTGGATACTGTCAAAGCTTCCCAATGGACCAGCTTATTATCCAAAGgcatgtcaag ... gaatttccagGATATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGA
EST: gi|9258756|gb|BE346903.1|BE346903
EST:     AGGACTGGATACTTTCAAAGCTTTCCAATGGACCAGCTTATTATCCANAG                         GATATTGTCAGTGAGCATGCAGAGAGA
genomic: AGGACTGGATACTGTCAAAGCTTCCCAATGGACCAGCTTATTATCCAAAGgcatgtcaag ... gaatttccagGATATTGTCAGTGAGCATCCAGAGAGA
EST: gi|214007313|gb|DB985849.1|DB985849
EST:     AGGACTGGATACTGTCAAAGCTTCCCAATGGACCAGCTTATTATCCAAAG                         G--ATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGA
genomic: AGGACTGGATACTGTCAAAGCTTCCCAATGGACCAGCTTATTATCCAAAGgcatgtcaag ... gaatttccagGATATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgcatacttttcatgtgctatgctaccttaatgttgttcctgaatttccagGATATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGAGAAAAGATTTTTATGCAGTATCGAAATGAAATTCCATATGCATGTCAG
                             ccttaat  putative branch site (score: 4)
                                                tttcc  putative PPT
       atactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaactttggatacaataagaaccaaaatatttcccttgtcatttcttctgcatacttttcatgtgctatgctaccttaatgttgttcctgaatttccagGATATTGTCAGTGAGCATCCAGAGAGATTTTTTGTAGCTGAAATTGTTAGAGAAAAGATTTTTATGCAGTATCGAAATGAAATTCCATATGCATGTCAG

- - - - - - - - - - -accaaaa
- - - - - - - - - - - - - - - - -cccttgt
- - - - - - - - - - - - - - - - - - - - - - - - - gcatact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt