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'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttcaaatgtttctgtaataagtaactcatgtgtttaacacagtcgtgttcaactttgaacaaattgctgatggttgctttgatatttttctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG

Basic information

species Zea mays
transcript GRMZM2G550865_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G550865_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 25
--ctttcaaatgtttctgtaataagtaactcatgtgtttaacacagtcgtgttcaactttgaacaaattgctgatggttgctttgatatttttctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG
    | || || | ||| |  |   | |  ||  |||||       ||    | |  ||| |   |   | |  |      | |    |  || | |  |||  | | |||| ||||||| || || |||||||| ||||||||||| | ||||||||||||||| ||||||||||||||||||| ||| |||||||| |||
aaagtgcatat-tatctttgtttgctcagcca-atgtttcttttgttcaaacttatttttaacagacaagttattaaccattatatgttccttgtttcctagCTCAAATGTTTATCCTGTCGTTGTGGCGGCACATCCTTCGGAAGCAAATCAGTTTGCTCTAGGCCTGACTGATGGTGGTGTTTATGTATTGGAACCCTTG
















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|211016175|gb|FL013379.1|FL013379
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATNCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTC
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCAT-CCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTC
EST: gi|113690337|gb|DW848599.1|DW848599
EST:     TCGGATTCTTCCAGCTTCGTATCT-CCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTAGTGGTTGCGGCACACCCTTCGGAAGCGAGTC
genomic: TCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTT-GTGGTTGCGGCACACCCTTCGGAAGCGAGTC
EST: gi|113836935|gb|DW958839.1|DW958839
EST:     TCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGNNAGT
genomic: TCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCG--AGT
EST: gi|19057713|gb|BM736380.1|BM736380
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|8665781|gb|BE186597.1|BE186597
EST:     TCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: TCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|19436915|gb|BM953325.1|BM953325
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|116814517|gb|EC857089.1|EC857089
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTAGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|87152457|gb|DY397246.1|DY397246
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|67024360|gb|CO453109.1|CO453109
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|19057573|gb|BM736240.1|BM736240
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|7304567|gb|AW600506.1|AW600506
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|88747083|gb|DY531224.1|DY531224
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|116819483|gb|EC862618.1|EC862618
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|4388094|gb|AI491266.1|AI491266
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|19436916|gb|BM953326.1|BM953326
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|7216838|gb|AW562960.1|AW562960
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGGTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|67032677|gb|CO461426.1|CO461426
EST:     GAACTTCA-TGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAA-TATCAG                         TCCGAGTGGTCATCCTG
genomic: GA-CTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTG
EST: gi|19437048|gb|BM953458.1|BM953458
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|31357352|gb|CD441709.1|CD441709
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|211400405|gb|FL382672.1|FL382672
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|60345367|gb|DN212340.1|DN212340
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|78083755|gb|DV512148.1|DV512148
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|6964703|gb|AW433396.1|AW433396
EST:     CTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: CTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
EST: gi|78083754|gb|DV512147.1|DV512147
EST:     AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAG                         TCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA
genomic: AGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 320

ATGCAAGCTTTATGGATGCCACTGTTGGCATATTTAATGCATCGAGTTTGAGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

ATGCAAGCTTTATGGATGCCACTGTTGGCATATTTAATGCATCGAGTTTGAGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 394

ATGCAAGCTTTATGGATGCCACTGTTGGCATATTTAATGCATCGAGTTTGAGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 289

ATGCAAGCTTTATGGATGCCACTGTTGGCATATTTAATGCATCGAGTTTGAGACTTCAATGTCGGATTCTTCCAGCTTCGTATCTCCCCCCAAATATCAGgtattctata ... tctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgttcaactttgaacaaattgctgatggttgctttgatatttttctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG
                                       tatttttctcttgt  CT-rich tract
                                  tttgatatttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttcaaatgtttctgtaataagtaactcatgtgtttaacacagtcgtgttcaactttgaacaaattgctgatggttgctttgatatttttctcttgtagTCCGAGTGTTCATCCTGTTGTGGTTGCGGCACACCCTTCGGAAGCGAGTCAGTTTGCTCTAGGGCTGACTGATGGTGGTGTTTTTGTGTTGGAACCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - tgtttct
- - - - - - - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - -aacacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatg