Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAAATATCAATGCCTCAAGCTCAAACAGCGATTCTGTTATGGCTGAAGCAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcagtttatcactgtccatcagttgaaactaaaaatgccctgacctgcctcaaatgcttcaagttttgatgactggttgtatgtactctcctga...

Basic information

species Zea mays
transcript GRMZM2G147671_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147671_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 5'ss of exon 6
CGAAAATAT---CAATGCCTCAAGCTCAAACAGCGATTCTGTTATGGCTGAAGCAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcagtttatcactgtccatcagt-tgaaactaaaaatgccctgacctgcctcaaatgcttcaagttttgatgactggttgtatgtactctcctga-
 |||||||    | |||||||||||||||||   |||||||||||||| ||||| |||| |||||||||||||||||    ||| ||  |||| ||||| |||||||| ||  | |   || ||  ||||          |||| | |    |   |  |   |||    |    |   | | |  || ||   |||      | 
TGAAAATAAGGACCATGCCTCAAGCTCAAACGCTGATTCTGTTATGGCAGAAGCGGAACCTGCCTCAAATGCTGCTG---ATGATAAAAAAGATCAGCCGAAGgtattgtcgttatcctacagttaatcatcacattgtgaaaagttctacaattggggtattatgtcatatagctatctaaatcattttaa--acttcatcaac
















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|5325058|gb|AI783249.1|AI783249
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|89252647|gb|DY624433.1|DY624433
EST:     GGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATTTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: GGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|9254597|gb|BE345080.1|BE345080
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCG
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCG
EST: gi|33094256|gb|CF054250.1|CF054250
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCA
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCA
EST: gi|60350002|gb|DN216975.1|DN216975
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|18964426|gb|BM660999.1|BM660999
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|24767864|gb|CA403000.1|CA403000
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|60401369|gb|DN234176.1|DN234176
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|32849896|gb|CD989577.1|CD989577
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTG
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTG
EST: gi|32942828|gb|CF047647.1|CF047647
EST:     CAGAACTTGCCTCANATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAG
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAG
EST: gi|4388150|gb|AI491322.1|AI491322
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|22542686|gb|BU093124.1|BU093124
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|76910327|gb|DV163809.1|DV163809
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|5846870|gb|AI999953.1|AI999953
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|32849329|gb|CD989010.1|CD989010
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATG
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATG
EST: gi|60400076|gb|DN232883.1|DN232883
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|37384426|gb|CF629283.1|CF629283
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|78021348|gb|DV489735.1|DV489735
EST:     CAGAACTTGCTTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|60352483|gb|DN219456.1|DN219456
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|18659918|gb|BM500591.1|BM500591
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGANAAGCAAGAACAGCCAAAG                         GNTGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGGAGGGC
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGG-AGGGC
EST: gi|67030433|gb|CO459182.1|CO459182
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|60395593|gb|DN228463.1|DN228463
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|87152942|gb|DY397731.1|DY397731
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|9733092|gb|BE511844.1|BE511844
EST:     ACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: ACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|9952492|gb|BE639075.1|BE639075
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTT
EST: gi|4804535|gb|AI665407.2|AI665407
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTG-CAAGCAAGAACAGCCAAAG                         GATGATGACGATCTA-TCCAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT

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), 47 (downstream exon)
Score: 263

CGAAAATATCAATGCCTCAAGCTCAAACAGCGATTCTGTTATGGCTGAAGCAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGTGCTTCAGGATCTGCAGCTGTGACTGACTCCGCTATGGCAGAAGCTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 320

CGAAAATATCAATGCCTCAAGCTCAAACAGCGATTCTGTTATGGCTGAAGCAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGTGCTTCAGGATCTGCAGCTGTGACTGACTCCGCTATGGCAGAAGCTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 321

CGAAAATATCAATGCCTCAAGCTCAAACAGCGATTCTGTTATGGCTGAAGCAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGTGCTTCAGGATCTGCAGCTGTGACTGACTCCGCTATGGCAGAAGCTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 290

CGAAAATATCAATGCCTCAAGCTCAAACAGCGATTCTGTTATGGCTGAAGCAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGTGCTTCAGGATCTGCAGCTGTGACTGACTCCGCTATGGCAGAAGCTGGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAAATATCAATGCCTCAAGCTCAAACAGCGATTCTGTTATGGCTGAAGCAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcagtttatcactgtccatcagttgaaactaaaaatgccctgacctgcctcaaatgcttcaagttttgatgactggttgtatgtactctcctga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC