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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTGGAGCCGAACTCCTCCGCACGGACACCCAATGCACGGATGCTTCCTTGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggtcgttctcgctttgtttcgccagttcgtagcttggcattgtggtgtctggctggtgttgaagttttgtggaaccgtgaattcag

Basic information

species Zea mays
transcript GRMZM2G423337_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423337_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g43930.2 (Oryza sativa), 5'ss of exon 16
CACTGGAGCCGAACTCCTCCGCACGGACACCCAATGCACGGATGCTTCCTTGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgt-aacttggtcgttctcgctttgtt-tcgccagttcgtagcttggcattgtggt-gtct-ggctggtgttgaagttttg--tggaaccgtgaattcag
||||||||| || ||||| ||||| ||| | ||| |||||||| |||||||||||||  ||||||||||||| || || ||||||||||| ||||||||||| |   ||||    ||   | | || ||||   | | ||  ||  |||||  ||  ||| ||||       || || ||  |    |     ||||||
CACTGGAGCGGATCTCCTTCGCACAGACTCACAAAGCACGGATTCTTCCTTGAAAGCAATGTGGCAACACTCTGATTCAATCATGTGCTGCTCCCTGAAGgtcagtgtggtgcgcctttttgtattgtcgctgatacata--tttacattgccgttatctaggctaacaaacaaattctggctactgcttaccattcag

upper sequence: GRMZM2G423337_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g43930.1 (Oryza sativa), 5'ss of exon 16
CACTGGAGCCGAACTCCTCCGCACGGACACCCAATGCACGGATGCTTCCTTGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgt-aacttggtcgttctcgctttgtt-tcgccagttcgtagcttggcattgtggt-gtct-ggctggtgttgaagttttg--tggaaccgtgaattcag
          || ||||| ||||| ||| | ||| |||||||| |||||||||||||  ||||||||||||| || || ||||||||||| ||||||||||| |   ||||    ||   | | || ||||   | | ||  ||  |||||  ||  ||| ||||       || || ||  |    |     ||||||
---------GGATCTCCTTCGCACAGACTCACAAAGCACGGATTCTTCCTTGAAAGCAATGTGGCAACACTCTGATTCAATCATGTGCTGCTCCCTGAAGGTCAGTGTGgtgcgcctttttgtattgtcgctgatacata--tttacattgccgttatctaggctaacaaacaaattctggctactgcttaccattcag
















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|60347903|gb|DN214876.1|DN214876
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|76912511|gb|DV164768.1|DV164768
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|71764261|gb|DR962198.1|DR962198
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|71298034|gb|DR784986.1|DR784986
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|4966813|gb|AI691669.1|AI691669
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|88756793|gb|DY540934.1|DY540934
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|60400862|gb|DN233669.1|DN233669
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|71298032|gb|DR784985.1|DR784985
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|32847407|gb|CD987088.1|CD987088
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|60401652|gb|DN234459.1|DN234459
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|60396119|gb|DN228988.1|DN228988
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|60354408|gb|DN221381.1|DN221381
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|78116184|gb|DV534571.1|DV534571
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|4804250|gb|AI666116.1|AI666116
EST:     CGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: CGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG

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), 49 (downstream exon)
Score: 376

CACTGGAGCCGAACTCCTCCGCACGGACACCCAATGCACGGATGCTTCCTTGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAGACGACGCTGATTGCGCTCCAGGACATCTCCCTTGAGAAGATCCTTGATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 84

CACTGGAGCCGAACTCCTCCGCACGGACACCCAATGCACGGATGCTTCCTTGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAGACGACGCTGATTGCGCTCCAGGACATCTCCCTTGAGAAGATCCTTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

CACTGGAGCCGAACTCCTCCGCACGGACACCCAATGCACGGATGCTTCCTTGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAGACGACGCTGATTGCGCTCCAGGACATCTCCCTTGAGAAGATCCTTGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 43

CACTGGAGCCGAACTCCTCCGCACGGACACCCAATGCACGGATGCTTCCTTGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAGACGACGCTGATTGCGCTCCAGGACATCTCCCTTGAGAAGATCCTTGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTGGAGCCGAACTCCTCCGCACGGACACCCAATGCACGGATGCTTCCTTGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggtcgttctcgctttgtttcgccagttcgtagcttggcattgtggtgtctggctggtgttgaagttttgtggaaccgtgaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG