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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACCACAAGTCATGCCAAGAATTTGCAGAGTTCTATAAGAACGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcaccatcaataacatttgaactgtaaaacaaaacttcagtttaaaagttcatctgacttattgactattctatatcttgtcag

Basic information

species Zea mays
transcript GRMZM2G083076_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083076_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 5'ss of exon 2
ATACCACAAGTCATGCCAAGAATTTGCAGAGTTCTATAAGAACGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcaccatcaataacatttgaactgtaaaacaaaacttcagttt---aaaagttcatctgacttattgactattctatatcttgtcag-------------------------------------
 ||||| ||| | ||||||||||| || || ||||||||||| |||||||| |||||||||||||| ||||||||||| || ||||||||||||||||| |||| |  ||    |||| ||||   |     |||| |  | |||    |   |  ||||  | | | | |     || | |  || ||||  |                                     
GTACCATAAGGCTTGCCAAGAATTCGCTGAATTCTATAAGAATGCTCTTCTTTATCTGGCCTACACTACTGTGGAGTCGCTCTCTGAGTCATTCAAGCTGgtat-taacaatgccaattacataacagaaaaaaaatagcatttcctcctctcattagttagtttaa-taacaacatactgtgcatattgtttgtattgataatttaccctttgacactgtcatgtgtcag

upper sequence: GRMZM2G083076_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 2
ATACCACAAGTCATGCCAAGAATTTGCAGAGTTCTATAAGAACGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcaccatcaataacatttgaactgtaaaacaaaacttcagtttaaaagttcatctgacttattgactattctatatct-tgtcag------------------------
 ||||| ||| |  ||||||||||||| |||||||| ||||| || ||||| |||||||| ||||| ||||| ||||| || |||||||| ||||| || |||||||  |   | || ||      || |  |  ||||||  ||| ||        |||     | ||    |||  |  |||| |||                           
GTACCATAAGGCTCGCCAAGAATTTGCTGAGTTCTACAAGAATGCCCTTCTGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttctattgttaacaatgc---aattacatgacaaaaaatcatttcctcctcgcattattttaataatgtatcttgcatctatgtttaccctttgatgctgtcttgtgtcag

upper sequence: GRMZM2G083076_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 2
ATACCACAAGTCATGCCAAGAATTTGCAGAGTTCTATAAGAACGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttc----accatcaataacatttgaactgtaaaacaaaacttcagtt-taaaagttcatctgacttattgactattctatatcttgtcag------
 |  || ||| || | ||||||||||| |||||||| || |  || ||||||||| |||| |||||| | ||||| ||||| ||||| ||||||||||| ||||||       |   ||   ||  |||    ||           ||  ||| |   |  |||  || ||  ||   | | || ||   ||          
GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatcagaattgtcttaaatgtttttgttgattgttgccttttttgttgtctcaaatca--tggctatttacttgtactttactctgattatggtgt

upper sequence: GRMZM2G083076_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G34310.1 (Glycine max), 5'ss of exon 2
ATACCACAAGTCATGCCAAGAATTTGCAGAGTTCTATAAGAACGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttc----accatcaataacatttgaactg-taaaacaaaacttcagtttaaaagttcatctgacttattgactattctata-tcttgtcag-----
 |  || ||| |||||||||||||||| |||||||| || |  || ||||||||| |||| |||||| | ||||| ||||| || || ||||||||||| ||||||       |   ||   ||  |||    || |         ||| | | |   |  |||  || ||  ||   ||  || || ||| || |      
GTTTCATAAGACATGCCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatcagaattgtcttaaatgtttttgttgattggttccttctttattgtctcaaatca--tggctatttacttacactgtactctggttatggcat

upper sequence: GRMZM2G083076_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 2
ATACCACAAGTCATGCCAAGAATTTGCAGAGTTCTATAAGAACGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcaccatcaataacatttgaactgtaaaacaaaacttcagtttaaaagttcatctgacttattgactattcta---tatcttgtcag-------
 ||  | || ||  | |||||||| ||||| |||||||| |  |||||||| |||||||| |||||| | ||||||||||| |||||  |||| ||||| ||||||| |  |||       | ||       ||||   || |    | |||   ||||  | |    || |||  |  |   | | ||| ||        
GTATTATAAATCTCGTCAAGAATTCGCAGAATTCTATAAAAGTGCTCTTCTATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttac-tcatgtgctttaattatttcaaaaaattcaagtcatttataatgattcacattatactttcacttgttaaggctgttttgacatctcatgt

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|78180907|gb|DV551280.1|DV551280
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATCCAAGCTA                         GACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttgtcagGACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
EST: gi|148930111|gb|EC872433.2|EC872433
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTTT
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttgtcagGACTTGGCTTTTGATCTTT
EST: gi|148994797|gb|EE034244.2|EE034244
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTA
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttgtcagGACTTGGCTTTT-GATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTA
EST: gi|12047287|gb|BF729426.1|BF729426
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATCCAAGCTA                         GACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttgtcagGACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
EST: gi|148960655|gb|EE011285.2|EE011285
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttgtcagGACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
EST: gi|8401231|gb|BE056865.1|BE056865
EST:     ATCTGG-CTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
genomic: ATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttgtcagGACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
EST: gi|149073975|gb|EE162304.2|EE162304
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttgtcagGACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
EST: gi|148999898|gb|EE036942.2|EE036942
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGGCTTT-GATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTA
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttgtcagGACTTGG-CTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTA
EST: gi|78103810|gb|DV522238.1|DV522238
EST:     CTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTNCA-GCTA                         GACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTA
genomic: CTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATT-CAAGCTAgtatgtttca ... atcttgtcagGACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTA
EST: gi|149111478|gb|EE294982.2|EE294982
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttgtcagGACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
EST: gi|148960706|gb|EE011347.2|EE011347
EST:     CTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCCATTCA-GCTA                         GACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
genomic: CTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTC-ATTCAAGCTAgtatgtttca ... atcttgtcagGACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
EST: gi|116829258|gb|EC866181.1|EC866181
EST:     TATCTAGGCCTAC-CAACTGTGGAGTCTCTATACTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT
genomic: TATCT-GGCCTACACAACTGTGGAGTCTCTAT-CTGAGTCATTCAAGCTAgtatgtttca ... atcttgtcagGACTTGGCTTTTGATCTTTCTCTAGCAGCCTTGCTGGGTGATAACATTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACCACAAGTCATGCCAAGAATTTGCAGAGTTCTATAAGAACGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcaccatcaataacatttgaactgtaaaacaaaacttcagtttaaaagttcatctgacttattgactattctatatcttgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT