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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaataccattattttcccctattactgttcaagaaatcactgttctgcatttttctggcaatataaacttatactgtgtcaatctcccctcatttcagGTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTATAACAATGCTCAGCTGTCTCCTCCAGGCCGAAGCCGTAGGTTTTATTCA

Basic information

species Glycine max
transcript GLYMA16G28200.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G28200.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g64700.2 (Oryza sativa), 3'ss of exon 5
tctaataccattattttcccctattactgttca--agaaatcactgttctgcatttttctggcaatataaacttatactgtgtcaatctcccctcatttcagGTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTATAACAATGCT-CAGCTGTCTCCTCCAGGCCGA--AGCCGTAGGTTTTATTCA
                     ||| | ||||||    | ||   | || | |||||| || |    ||||   ||||      | | | |      || |||||||||||| || ||||| || |||||||||||||| |||||||| || || ||    |||  ||       |  | |   ||  |||   || ||| |    
----------------gtaattatca-tgttcattgaagatggttattttccattttgcttgtttcataa---tatataaaccctagcactgtcatttccagGTCAAATTTCCTTGGCACAAAATTTATAATTTATGACACACAGCCCCCTTACAATGGGGCTGTAGTCCCTCACGTCGGAAGGACCAGCAAGAGATTTAAC---

upper sequence: GLYMA16G28200.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
--tctaataccattattttcccctattactgttcaagaaatcactgttctgcatttttctggcaatataaacttatactgtgtcaatct--cccctcatttcagGTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTATAACAATGCTCAGCTGTCTCCTCCAGGCCGAA---GCCGTAGGTTTTATTCA
  | | |   ||  |||||    |    |   | |   | |   |||||   |  || ||  | || |   || | | | |||   ||   |||||  ||||||||||||||| || ||||| ||||| |||||||||||||||||||| || || ||   | |||| || || || || |||||||   |||| ||||| ||    
tatttcaggtca--atttttgttttaagcctataatctagtttgtgttc-ataaattactctctatctgt-ctcaaaatttgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC---
















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|193637880|gb|FK585738.1|FK585738
EST:     GATGCGGATAACGTATCAAGATCTAATAGCACTTACATTGGAAAACTCAG                         GTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTA
genomic: GATGCGGATAACATATCAAGATCTAATAGCACTTACATTGGAAAACTCAGgtatattctc ... ctcatttcagGTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTA
EST: gi|151394298|gb|EV264169.1|EV264169
EST:     GATGCGGATAACATATCAAGATCTAATAGCACTTACATTGGAAAACTCAG                         GTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTA
genomic: GATGCGGATAACATATCAAGATCTAATAGCACTTACATTGGAAAACTCAGgtatattctc ... ctcatttcagGTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTA
EST: gi|254340191|gb|GR858316.1|GR858316
EST:     GATGCGGATA-CATATCA-GATCTAATAGCACTTACATTGGAAAACTCAG                         -TCAAATTTTCTCG
genomic: GATGCGGATAACATATCAAGATCTAATAGCACTTACATTGGAAAACTCAGgtatattctc ... ctcatttcagGTCAAATTTTCTCG
EST: gi|192295189|gb|FG986908.1|FG986908
EST:     GATGCGGATAACATATCAAGATCTAATAGCACTTACATTGGAAAACTCAG                         GTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTA
genomic: GATGCGGATAACATATCAAGATCTAATAGCACTTACATTGGAAAACTCAGgtatattctc ... ctcatttcagGTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTA
EST: gi|7588744|gb|AW704533.1|AW704533
EST:     GATGCGGATAACATATCAAGATCTAATAGCACTTACATTGGAAAACTCAG                         GTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTA
genomic: GATGCGGATAACATATCAAGATCTAATAGCACTTACATTGGAAAACTCAGgtatattctc ... ctcatttcagGTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgcatttttctggcaatataaacttatactgtgtcaatctcccctcatttcagGTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTATAACAATGCTCAGCTGTCTCCTCCAGGCCGAAGCCGTAGGTTTTATTCA
                                       tctcccctcatttc  CT-rich tract
                aatataaacttatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctaataccattattttcccctattactgttcaagaaatcactgttctgcatttttctggcaatataaacttatactgtgtcaatctcccctcatttcagGTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTATAACAATGCTCAGCTGTCTCCTCCAGGCCGAAGCCGTAGGTTTTATTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - tttcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atctccc