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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagcagccattagagatgtgagacgagatctggaaaccattgtgcattggtttagcattgctctacgaagttccttattgtgcaaagtttgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGATTAAATCAGAAG

Basic information

species Zea mays
transcript GRMZM2G169773_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 5
ctagcagccattagagatgtgagacgagatctggaaaccatt-gtgcattggtttagcattgctctacgaagtt---ccttattgtgcaaagttt---gttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGATTAAATCAGAAG
         | |  |  |  |    |||| || | | | ||| |    ||||| |||||||||||||| ||| |    ||||||||||||| |||   || ||||||||||| | || || || || |||||||| |||||||||||||||||||||||||||   | ||
-------ggactgaattttggttgtgagagctagtacctatttgcatgttggtgtagcattgctctacaaagctgcttcttattgtgcaaactttgatgtcatgcagGATTGGCGGCATGTCTTTTCTGGAACATAATTGCAACTACAGCAGCATGGATTAAAGGGGCAG
















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|148980186|gb|EE026996.2|EE026996
EST:     ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGG                         GATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
genomic: ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
EST: gi|211370168|gb|FL333601.1|FL333601
EST:     ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGG                         GATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
genomic: ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
EST: gi|76293307|gb|DV032875.1|DV032875
EST:     ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGG                         GATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
genomic: ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
EST: gi|76293306|gb|DV032874.1|DV032874
EST:     AATTCACCTGCAAAGGATGCAGTACCGGGCGTTTTCTTCACTATTGG                         GATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
genomic: AATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
EST: gi|71429331|gb|DR810381.1|DR810381
EST:     ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGG                         GATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
genomic: ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
EST: gi|71449251|gb|DR830301.1|DR830301
EST:     ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGG                         GATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
genomic: ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
EST: gi|211012583|gb|FL327130.1|FL327130
EST:     ACCAATTCACCTGYWAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGG                         GAATTGACAGCTTG
genomic: ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGA-TTGACAGCTTG
EST: gi|78115059|gb|DV533447.1|DV533447
EST:     ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGG                         GATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
genomic: ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
EST: gi|78115058|gb|DV533446.1|DV533446
EST:     GCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGG                         GATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
genomic: GCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
EST: gi|78077114|gb|DV505548.1|DV505548
EST:     ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGG                         GATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
genomic: ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
EST: gi|78077113|gb|DV505547.1|DV505547
EST:     ACCAATTCACCTGCAAAGGAAGCAGTACCTGGCGTTTTCTTCACTATTGG                         GATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
genomic: ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA
EST: gi|211146797|gb|FL347631.1|FL347631
EST:     ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGG                         GATTGACAGCTTGCCTCTTTTGGA-CATCATTGCAACTACAGCAGCATGGA
genomic: ACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGA

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: 45 (upstream exon), 46 (downstream exon)
Score: 55

AATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGATTAAATCAGAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 143

AATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGATTAAATCAGAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 235

AATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGATTAAATCAGAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 136

AATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTACCTGGCGTTTTCTTCACTATTGGgtaagtgtcg ... tgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGATTAAATCAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattggtttagcattgctctacgaagttccttattgtgcaaagtttgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGATTAAATCAGAAG
                                           tttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagcagccattagagatgtgagacgagatctggaaaccattgtgcattggtttagcattgctctacgaagttccttattgtgcaaagtttgttatgcagGATTGACAGCTTGCCTCTTTTGGAACATCATTGCAACTACAGCAGCATGGATTAAATCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
-tagcagc
- - - - - - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattgc