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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgattcgctcccatgctgcccgcaaacggtctgatcgagctgattgactgattgacgctgtgatgtcggctgacctggctcctgtgtcgcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACCACGGGATCGGGAATGGAGGGCCCGCCGACGGCGAGCAAAGCTGGTGGGG

Basic information

species Zea mays
transcript GRMZM2G152056_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152056_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g50870.1 (Oryza sativa), 3'ss of exon 2
ttcgattcgctcccatgctgcccgcaaacggtctgatcgagctgattgactgattgacgctgtgatgtc-ggctgacctg-gctcctg---------tgtcgcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACCACGGGATCGGGAATGGAGGGCCCGCCGACGGCGAGCAAAGCTGGTGGGG
            |  |||     |  || |   |    ||    | |  ||| |||     |  |  || || |||  |  ||| |||         | || |||| |||||| ||||| |||||||||||||||||||||||||||||||| |||||||| ||||| ||||| |||||||||||||| | |||   |   |  || |   
-----------tctttgcaatttgtgaatgactttgatgatgaaaatagctgtttgttttggccagatcaggttgatttatgctgctgacgttgtcatctctcatctgcagGATGCGGCCATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGGGGCTGGACGACGGGGTCGGGGATGGAGGGCCCGCCCAAGGCCGCCGGTGGGGGAGACC
















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|211308767|gb|FL253751.1|FL253751
EST:     AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAG                         GACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
genomic: AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
EST: gi|211308771|gb|FL253755.1|FL253755
EST:     AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAG                         GACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
genomic: AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
EST: gi|211308766|gb|FL253750.1|FL253750
EST:     AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAG                         GACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
genomic: AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
EST: gi|37422189|gb|CF648800.1|CF648800
EST:     AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAG                         GACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
genomic: AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
EST: gi|211308770|gb|FL253754.1|FL253754
EST:     AGCCCACTAGCCTGGCGCCGTACGGCATCTCCATCTCGCCGCTCTCCAAG                         GACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
genomic: AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
EST: gi|211306744|gb|FL253741.1|FL253741
EST:     GCCCACTCAGCCTGGCGCCGTACGGCATCTCCATCTCGCCGCTCTCCAAG                         GACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
genomic: GCCCACT-AGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
EST: gi|211308775|gb|FL253759.1|FL253759
EST:     AGCCCACTAGCCTGGCGCCGTACGGCATCTCCATCTCGCCGCTCTCCAAG                         GACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
genomic: AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
EST: gi|211306745|gb|FL253742.1|FL253742
EST:     AGCCCACTAGCCTGGCGCCGTACGGCATCTCCATCTCGCCGCTCTCCAAG                         GACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
genomic: AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
EST: gi|211306750|gb|FL253747.1|FL253747
EST:     AGCCCACTAGCCTGGCGCCGTACGGCATCTCCATCTCGCCGCTCTCCAAG                         GACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC
genomic: AGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACC

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: 48 (upstream exon), 41 (downstream exon)
Score: 33

CGAAGACGACAAGGAGACCGCTAAAGGTTCCGGCTCGGAACCCCGGCGCGAGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACCACGGGATCGGGAATGGAGGGCCCGCCGACGGCGAGCAAAGCTGGTGGGG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 47

CGAAGACGACAAGGAGACCGCTAAAGGTTCCGGCTCGGAACCCCGGCGCGAGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACCACGGGATCGGGAATGGAGGGCCCGCCGACGGCGAGCAAAGCTGGTGGGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 35

CGAAGACGACAAGGAGACCGCTAAAGGTTCCGGCTCGGAACCCCGGCGCGAGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACCACGGGATCGGGAATGGAGGGCCCGCCGACGGCGAGCAAAGCTGGTGGGG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 57

CGAAGACGACAAGGAGACCGCTAAAGGTTCCGGCTCGGAACCCCGGCGCGAGCCCACTAGCCTGGCGCCGTATGGCATCTCCATCTCGCCGCTCTCCAAGgtacggacgc ... gcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACCACGGGATCGGGAATGGAGGGCCCGCCGACGGCGAGCAAAGCTGGTGGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactgattgacgctgtgatgtcggctgacctggctcctgtgtcgcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACCACGGGATCGGGAATGGAGGGCCCGCCGACGGCGAGCAAAGCTGGTGGGG
                        ggctgac  putative branch site (score: 57)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcgattcgctcccatgctgcccgcaaacggtctgatcgagctgattgactgattgacgctgtgatgtcggctgacctggctcctgtgtcgcatcggcagGACGCGGCTATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGCGGCTGGACCACGGGATCGGGAATGGAGGGCCCGCCGACGGCGAGCAAAGCTGGTGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - atgctgc
- - - - - - - - - - - - - - - - - - - - -ctgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacctg