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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAGCGAATGAAACTGGAGAAGCTGCAGCAATACCAATTACTGTGAGGCAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACTgtaagtattgctgttattctttattacactttgtaccttttatccgaaactcttagtgcaatttcatgaaaaaatatgaatacagtcagtgcctgcatgg...

Basic information

species Glycine max
transcript GLYMA17G11220.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11220.1 (Glycine max), 5'ss of exon 15
lower sequence: GRMZM2G450055_T01 (Zea mays), 5'ss of exon 16
AACAAGCGAATGAAACTGGAGAAGCTGCAGCAATACCAATTACTGTGAGGCAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACTgtaagtattg--ctgttattctttattacactttgtaccttttatccgaaactcttagtgcaatttcat-gaaaaaatatgaatacagtcagtgcctgcatgg-------
| |||||  | || || ||    |||||||||||||| || |||||||||||||| ||||| ||  |  | ||||||||  | ||||||||||||| | |||||||| |   || | |   | | |||     |  | |   ||    | |   |  |     |||||  |    | |      |  |    || ||| |||        
AGCAAGCTCACGAGACAGGGAGGGCTGCAGCAATACCCATCACTGTGAGGCAGCTTGAAGCCATCATACGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtactagactatcaca-tgtgttatgacattgatcacatactgcatatattctgcctcctttcaccgtttcattgcactcatggctgatgtctgaatgactcttag

upper sequence: GLYMA17G11220.1 (Glycine max), 5'ss of exon 15
lower sequence: AT2G07690.2 (Arabidopsis thaliana), 5'ss of exon 15
AACAAGCGAATGAAACTGGAGAAGCTGCAGCAATACCAATTACTGTGAGGCAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACTgtaagtattgctgttattctttattacactttgtaccttttatccgaaactcttagtgcaatttcatgaaaaaatatgaatacagtcagtgcctgcatgg
 ||  ||  ||||||| ||||| |||||  | ||||| || || ||||| || || ||||||||||| ||  |||||||| |||||||||| |||| |||||||||| |  | |||  | |    |  | |  | |||   | | ||     |  ||||  |    ||| |   | | ||||  |||||           
GACGTGCACATGAAACAGGAGAGGCTGCTCCGATACCTATCACAGTGAGACAACTCGAAGCTATTGTCAGACTGAGTGAGTCACTTGCAAAAATGAGACTgtaagtaatcttattaa-catagagattcctgattcctgaaacctgatgggat--gtgccgtccattgacattgt-taaatat-gtcag-----------

upper sequence: GLYMA17G11220.1 (Glycine max), 5'ss of exon 15
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 5'ss of exon 15
AACAAGCGAATGAAACTGGAGAAGCTGCAGCAATACCAATTACTGTGAGGCAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACTgtaagtattgctgttattctttattacactttgtaccttttatccgaaactcttagtgcaatttcatgaaaaaatatga-atacagtcagtgcctgcatgg---
| ||||| ||||||||||| || || || || |||||||||||||| || || || |||||||| || ||||| |||||||||||||||||||||| |||||||||| || ||| |   |||   |   |   ||    |||   |   ||| |      | | |   ||| |  |  | ||| | | | ||   ||| ||   
AGCAAGCAAATGAAACTGGGGAGGCAGCTGCCATACCAATTACTGTAAGACAACTAGAAGCTATCGTAAGGTTAAGTGAGGCACTTGCAAAGATGAGACTgtaagtactggtgt-agaatttgacagtttgcatagtccttaattg---ctcatgaaaataatactcaaaatatcaaaagataaattgattgatggcaagggtt

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|193654575|gb|FK597885.1|FK597885
EST:     CAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACT                         ATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGCTTTTCAC
genomic: CAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACTgtaagtattg ... cttgcaccagATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGCTTTTCAC
EST: gi|15814447|gb|BI786722.1|BI786722
EST:     CAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACT                         ATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGCTTTTCAC
genomic: CAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACTgtaagtattg ... cttgcaccagATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGCTTTTCAC
EST: gi|193363739|gb|FK331337.1|FK331337
EST:     AGCTGGAAGCTATTGTTAGGTTTGAGTGAGGCACTTGCAAAGATGAAACT                         ATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGCTTTTTCA
genomic: AGCTGGAAGCTATTGTTAGG-TTGAGTGAGGCACTTGCAAAGATGAAACTgtaagtattg ... cttgcaccagATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGC-TTTTCA
EST: gi|22932051|gb|BU549190.1|BU549190
EST:     CAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACT                         ATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGCTTTTCAC
genomic: CAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACTgtaagtattg ... cttgcaccagATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGCTTTTCAC
EST: gi|193342503|gb|FK307323.1|FK307323
EST:     CAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACT                         ATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGCTTTTCAC
genomic: CAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACTgtaagtattg ... cttgcaccagATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGCTTTTCAC
EST: gi|207838896|gb|GD813400.1|GD813400
EST:     CAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACT                         ATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGCTTTTCAC
genomic: CAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACTgtaagtattg ... cttgcaccagATCTCATCTTGCTACTGAGGAGAATGTGCAAGAAGCAGTAAGGCTTTTCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAAGCGAATGAAACTGGAGAAGCTGCAGCAATACCAATTACTGTGAGGCAGCTGGAAGCTATTGTTAGGTTGAGTGAGGCACTTGCAAAGATGAAACTgtaagtattgctgttattctttattacactttgtaccttttatccgaaactcttagtgcaatttcatgaaaaaatatgaatacagtcagtgcctgcatgg

- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaaaaaa