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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcatctcccccttgtgcttctttataaatttttgaaatcaacttaatatatcttttagaaacttgagtttggatatcttttatgtagGTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTCCCTTCTATGCACTTATCCCCTGAGGATGTACGATGGATG

Basic information

species Glycine max
transcript GLYMA07G38890.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 15
lower sequence: AT1G61850.2 (Arabidopsis thaliana), 3'ss of exon 16
----gtatatcatctcccccttgtgcttctttataa-atttttgaaatcaacttaatatatcttttagaaacttgagtttggatatc--ttttatgtagGTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTCCCTTCTATGCACTTATCCCCTGAGGATGTACGATGGATG
    | ||||  | | |   ||   ||||||| |    ||  ||  ||    || | |  | | ||  |   ||||  ||   | |   | |  ||||||| ||||||||||||||||||||||| || | |||||| || || ||||| |||||    |||||  | ||||| ||| | || ||||||
gtaagaatat-gttttcatatta-acttctttgtggtgttactgttatagcgttgaaagctttattttatttttgatgttacttgttaatatactgtagGTGATGGAAGATGATCAAGAAATTGCATCGTTTATGTTCCGCAGAACTGTACCTTCGGCACACTTGACTCCTGATGATATTCGCTGGATG

upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 16
gtatatcatctcccccttgtgcttctttataaatttttgaaatcaacttaatatatcttttagaaacttgagtttggatatcttttatgtagGTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTCCCTTCTATGCACTTATCCCCTGAGGATGTACGATGGATG
   |||    || | ||||||| |   |     || |||  |  |  ||   ||  ||  ||  |   || | |            ||  |||||||||||||||||||||||||||   |||| |||||||| || || || |||||| |||||||| |  |||| ||||| || ||||||
--gtat-gcttctcacttgtgccttcctt----ttgttgctaataggtt--catgactactaacattctgtgat------------attaagGTTATGGAAGATGATCAAGAAATTGGGGCATACATGTTTCGAAGAACAGTTCCTTCTTTGCACTTAACGGCTGATGATGTTCGTTGGATG
















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|208293137|gb|GE096387.1|GE096387
EST:     ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTT                         GTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTC
genomic: ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTTgtatatcatc ... ttttatgtagGTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTC
EST: gi|193525538|gb|FK478047.1|FK478047
EST:     ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTT                         GTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTC
genomic: ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTTgtatatcatc ... ttttatgtagGTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTC
EST: gi|193361269|gb|FK328629.1|FK328629
EST:     ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTT                         GTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTC
genomic: ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTTgtatatcatc ... ttttatgtagGTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTC
EST: gi|13481690|gb|BG511033.1|BG511033
EST:     ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTT                         GTTATGGAAGATGATCAAGAAATTGCTTCATATATGGTTCGTAGGACTGGC
genomic: ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTTgtatatcatc ... ttttatgtagGTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTC
EST: gi|51335705|gb|CO979571.1|CO979571
EST:     ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTT                         GTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTC
genomic: ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTTgtatatcatc ... ttttatgtagGTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTC
EST: gi|193653530|gb|FK599528.1|FK599528
EST:     ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTT                         GTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTC
genomic: ATTTCCAAATTGGAGGCATTGTCCACCGTTATCTAGGCCGTCAAACCCTTgtatatcatc ... ttttatgtagGTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatcaacttaatatatcttttagaaacttgagtttggatatcttttatgtagGTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTCCCTTCTATGCACTTATCCCCTGAGGATGTACGATGGATG
        acttaat  putative branch site (score: 4)
                                         tatctttt  putative PPT
       aacttaatatatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatcatctcccccttgtgcttctttataaatttttgaaatcaacttaatatatcttttagaaacttgagtttggatatcttttatgtagGTTATGGAAGATGATCAAGAAATTGCTTCATATATGTTTCGTAGGACTGTCCCTTCTATGCACTTATCCCCTGAGGATGTACGATGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA