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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCCGCCCGCTCCGCTGAGGACGCGGGCGATGGCTTCGGGATCGACATCGAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaaccccaggcccctcgtccctcttctctcttctcgccgctaggggagcgctcagtattctcctaggccctgcgcgataggagcagagctaact...

Basic information

species Zea mays
transcript GRMZM5G817035_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G817035_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g40630.1 (Oryza sativa), 5'ss of exon 1
CTGCCGCCCGCTCCGCTGAGGACGCGGGCGATGGCTTCGGGATCGACATCGAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaaccccaggcccctcgtccctcttctctcttctcgccgctaggggagcgctcagtattctcctaggccctgcgcgataggagcagagctaact
| || |        |  || | ||  || |  ||||||||||||||||||||||| ||||||||||||||||||||||||||| ||||||||||||||||||| | | |  ||   || | | || ||| || ||    |   | ||||    || |  ||         |   |    || |  |   |   |      
CCGCGGAGGAGGAGGAGGACGGCGGCGGGGGAGGCTTCGGGATCGACATCGAGGCCGCCGTCCGCTCCGCCAACGACCGCGTCTCCGGCACCTTCGGCGTgtaagcataatccccccctcccttctctcctccctagggtttgcactagattcgccccgagctaagcttaatctcacttgcaactgcgtctcggtaggga
















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|211250255|gb|FL081796.1|FL081796
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTGCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|28568996|gb|CB280871.1|CB280871
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|149040600|gb|EE046841.2|EE046841
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|211310097|gb|FL216550.1|FL216550
EST:     CGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAA
genomic: CGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTT-AAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAA
EST: gi|211248039|gb|FL081793.1|FL081793
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|78082562|gb|DV510974.1|DV510974
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|60342132|gb|DN209105.1|DN209105
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|71425789|gb|DR806892.1|DR806892
EST:     TCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTG-TAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: TCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|211250260|gb|FL081801.1|FL081801
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTSSCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|211250256|gb|FL081797.1|FL081797
EST:     AGGCGGCCGTCTC-CTCCGCTAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: AGGCGGCCGTC-CGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|211250258|gb|FL081799.1|FL081799
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTGCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|211250253|gb|FL081794.1|FL081794
EST:     GAGACGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTGCCAGGCAGCTTTAAGTCTACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|211250257|gb|FL081798.1|FL081798
EST:     GAGACGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTGCCAGGCAGCTTTAAGTCTACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|211250259|gb|FL081800.1|FL081800
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|211248036|gb|FL081790.1|FL081790
EST:     GAGACGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTGCCAGGCAGCTTTAAGTCTACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|74236299|gb|DT644213.1|DT644213
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|71425790|gb|DR806893.1|DR806893
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
EST: gi|211248037|gb|FL081791.1|FL081791
EST:     GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGT                         GGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG
genomic: GAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAG

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: 107

CTGCCGCCCGCTCCGCTGAGGACGCGGGCGATGGCTTCGGGATCGACATCGAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAGCAGTGTTCCATCTGGCAGATCTCTCATGTATTTCGGTCTGTTTCTTGGT


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 61

CTGCCGCCCGCTCCGCTGAGGACGCGGGCGATGGCTTCGGGATCGACATCGAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAGCAGTGTTCCATCTGGCAGATCTCTCATGTATTTCGGTCTGTTTCTTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

CTGCCGCCCGCTCCGCTGAGGACGCGGGCGATGGCTTCGGGATCGACATCGAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAGCAGTGTTCCATCTGGCAGATCTCTCATGTATTTCGGTCTGTTTCTTGGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 60

CTGCCGCCCGCTCCGCTGAGGACGCGGGCGATGGCTTCGGGATCGACATCGAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaac ... atttgtccagGGTCTCAAAAGGTGTTAAAGGGTTTCCAGGCAGCTTTAAGTCCACAACAAGCAGTGTTCCATCTGGCAGATCTCTCATGTATTTCGGTCTGTTTCTTGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCCGCCCGCTCCGCTGAGGACGCGGGCGATGGCTTCGGGATCGACATCGAGGCGGCCGTCCGCTCCGCCAACGACCGCGTCGCCGGCACCTTCGGCGTgtacgtaaaccccaggcccctcgtccctcttctctcttctcgccgctaggggagcgctcagtattctcctaggccctgcgcgataggagcagagctaact

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