Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatttgttttattctaagataagatttttatgtttgactgttatataaatgtttcttgccaatggacctcccttaagtatctcatagtttagga...

Basic information

species Zea mays
transcript GRMZM2G153087_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153087_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G14510.1 (Arabidopsis thaliana), 5'ss of exon 3
AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatttgttttattctaagat--aagatttttatgtttgactgttatataaatgtttcttgccaatggacctcccttaagtatctcatagtttagga
||||||| ||| | ||  | |||||||| || |||||||| ||||| || |||||||||||||| ||||| ||| | || ||||| |  ||  |    |||||      ||  | |  ||   | |    | || |||  ||||  ||||   ||||  ||   || | |      |  ||  |  ||   |   |  |   
AAAAAGACTGGATTTCTTTGGTTGCAGTTCACAGTGATTCATGGCTTATCTCTGTTGCATTTTACTTTGGTGCACGTTTCGGATTTGGCAAGAATGAGAGgtaagtttctttctctgctcagtgttctgtgtttgttaattttgcttgtttggtaaagcttcaatgactagtatagtagctgcataattctagcatccaa--
















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|211265771|gb|FL248408.1|FL248408
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCT
EST: gi|76292992|gb|DV032560.1|DV032560
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|211265767|gb|FL248404.1|FL248404
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGA-TCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCC-AGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|76282003|gb|DV021571.1|DV021571
EST:     GCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: GCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|71326250|gb|DR799818.1|DR799818
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|211265779|gb|FL248416.1|FL248416
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|76282004|gb|DV021572.1|DV021572
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|211268204|gb|FL248420.1|FL248420
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGA
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGA
EST: gi|71772104|gb|DR970041.1|DR970041
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|149014987|gb|EE044728.2|EE044728
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|78090616|gb|DV518990.1|DV518990
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|78075129|gb|DV503563.1|DV503563
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|113703593|gb|EE681097.1|EE681097
EST:     GGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: GGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|211268203|gb|FL248419.1|FL248419
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|76013927|gb|DT941097.1|DT941097
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|31357900|gb|CD442257.1|CD442257
EST:     GCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|71311485|gb|DR792097.1|DR792097
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|76292991|gb|DV032559.1|DV032559
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|71326247|gb|DR799817.1|DR799817
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|211265778|gb|FL248415.1|FL248415
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|211268206|gb|FL248422.1|FL248422
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|78090615|gb|DV518989.1|DV518989
EST:     TCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
EST: gi|211265780|gb|FL248417.1|FL248417
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCT
EST: gi|71311486|gb|DR792098.1|DR792098
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 113

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGCCCAAAGAAAAAACTCCTAAAAGCAAC


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 127

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGCCCAAAGAAAAAACTCCTAAAAGCAAC


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 139

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGCCCAAAGAAAAAACTCCTAAAAGCAAC


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 56

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatt ... ttgcttgcagGAAACGTCTCTTCACCATGATCAATAACCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGCCCAAAGAAAAAACTCCTAAAAGCAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGATAAAGAATCCAGgtattccatttgttttattctaagataagatttttatgtttgactgttatataaatgtttcttgccaatggacctcccttaagtatctcatagtttagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagataag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctccctt