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'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcatacatttcctaatatcgtaatatttttttcatttggtcttctttgattcacttggggtccttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTCTGTCGAAATGGCTGAT

Basic information

species Zea mays
transcript GRMZM2G071071_T01
intron # 9
splice site 3'
intron type U2

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|31359528|gb|CD443885.1|CD443885
EST:     GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATGATTCATCGGAAG                         GCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|67019644|gb|CO448393.1|CO448393
EST:     GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAG                         GCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|17970264|gb|BM277027.1|BM277027
EST:     CTACAATCATTCATCGGAAG                         GCAACCTTCTGAAGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: CTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|32841088|gb|CD980769.1|CD980769
EST:     ATCGTTGCTACAATCATTCATCGGAAG                         GCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: ATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|67017730|gb|CO446479.1|CO446479
EST:     GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAG                         GCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|32840298|gb|CD979979.1|CD979979
EST:     GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAG                         GCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|31356495|gb|CD440852.1|CD440852
EST:     GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAG                         GCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|32839739|gb|CD979420.1|CD979420
EST:     ACATCGTTGCTACAATCATTCATCGGAAG                         GCACCCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: ACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|87152121|gb|DY396910.1|DY396910
EST:     GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAG                         GCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|32839495|gb|CD979176.1|CD979176
EST:     GTGCCAGAGGCTCT-GAAAGACCATCGTTGCTACAATCATTCATCGGAAG                         GCAACCCTTCTGATGCCCTGCCATCTAACAGCGAACGC-TTGCAACAAATT
genomic: GTGCCAGAGGCTCTGGAAAGA-CATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAA-CCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATT
EST: gi|18384193|gb|BM417393.1|BM417393
EST:     GCTACAATCATTCATCGGAAG                         GCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: GCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|18385253|gb|BM418452.1|BM418452
EST:     GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAG                         GCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|32839754|gb|CD979435.1|CD979435
EST:     GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAG                         GCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
genomic: GGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC
EST: gi|32933393|gb|CF038205.1|CF038205
EST:     ATCGTTGCTACAATCATTCATCGGAAG                         GCAACCTTCTGATGCCCTGCCATCTAACGGCGAACGCTTTGCAACAAATTC
genomic: ATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTC

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), 48 (downstream exon)
Score: 244

ATCGTAAAAAGCAACAGACACAGAGAAACATTTTCCAGTGTTTTGTTTTCGGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTCTGTCGAAATGGCTGAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 240

ATCGTAAAAAGCAACAGACACAGAGAAACATTTTCCAGTGTTTTGTTTTCGGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTCTGTCGAAATGGCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 265

ATCGTAAAAAGCAACAGACACAGAGAAACATTTTCCAGTGTTTTGTTTTCGGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTCTGTCGAAATGGCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

ATCGTAAAAAGCAACAGACACAGAGAAACATTTTCCAGTGTTTTGTTTTCGGTGCCAGAGGCTCTGGAAAGACATCGTTGCTACAATCATTCATCGGAAGgtatgtcata ... cttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTCTGTCGAAATGGCTGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtaatatttttttcatttggtcttctttgattcacttggggtccttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTCTGTCGAAATGGCTGAT
                          ctttgat  putative branch site (score: 269)
                                           tccttgt  putative PPT
     atatttttttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcatacatttcctaatatcgtaatatttttttcatttggtcttctttgattcacttggggtccttgtaacagGCAACCTTCTGATGCCCTGCCATCTAACAGCGAACGCTTTGCAACAAATTCTGTCGAAATGGCTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT