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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTGCTGGTGGGAATTCAGCAACCGAACCTTACATAGTTGCTCATAATTTTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccatcttgagaacctcagaagttcctctgaaaaataacatcactctagcactcctaggagtggtaaactgatgttattttattcaatgaagtgt...

Basic information

species Zea mays
transcript GRMZM2G118003_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118003_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g49600.1 (Oryza sativa), 5'ss of exon 6
CGCTGCTGGTGGGAATTCAGCAACCGAACCTTACATAGTTGCTCATAATTTTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccatcttgagaacctcagaagttcctctgaaa---aataacatcactctagcactcctaggagtggtaaactgatgttattttattcaatgaagtgt
||||||||||||||| |||||||| ||||| ||||| ||||||||||||||||||||  |||||||| | || |||||||||||||| || || ||||||||||||   ||| ||     |    || |  | | |     | | |  ||| || |  ||  | |  |||| || | | ||  ||          |||  | |
CGCTGCTGGTGGGAACTCAGCAACAGAACCATACATTGTTGCTCATAATTTTCTCTTATCACATGCTGCAGCTGTTGCAAGATACCGGACTAAGTATCAGgtattttt-tctcgacttgttttttagataatttaagctttattgaactcagtcaattacatcaa--agtgatacaatcatactaagaacacttctgacctct
















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|22546685|gb|BU098996.1|BU098996
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
EST: gi|87157163|gb|DY401952.1|DY401952
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
EST: gi|6826935|gb|AW330578.1|AW330578
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACAAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAA
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAA
EST: gi|31611947|gb|CD568569.1|CD568569
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
EST: gi|211416183|gb|FL300110.1|FL300110
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAMATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
EST: gi|18659314|gb|BM500272.1|BM500272
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
EST: gi|5268889|gb|AI770853.1|AI770853
EST:     TTCTCTTGGCACATGCTACTGAAGTTGCAAGATACCGTACGAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
EST: gi|29543733|gb|CB604113.1|CB604113
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
EST: gi|60350347|gb|DN217320.1|DN217320
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
EST: gi|21760120|gb|BQ635661.1|BQ635661
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
EST: gi|31359746|gb|CD444103.1|CD444103
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGGACGAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
EST: gi|31353887|gb|CD438244.1|CD438244
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
EST: gi|211416180|gb|FL300107.1|FL300107
EST:     TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAG                         GCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG
genomic: TTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAG

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: 1034

CGCTGCTGGTGGGAATTCAGCAACCGAACCTTACATAGTTGCTCATAATTTTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAGGCTCTTACAAACTCACCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 915

CGCTGCTGGTGGGAATTCAGCAACCGAACCTTACATAGTTGCTCATAATTTTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAGGCTCTTACAAACTCACCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

CGCTGCTGGTGGGAATTCAGCAACCGAACCTTACATAGTTGCTCATAATTTTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAGGCTCTTACAAACTCACCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 596

CGCTGCTGGTGGGAATTCAGCAACCGAACCTTACATAGTTGCTCATAATTTTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccat ... aaaaacatagGCTGCTCAGAAGGGTAAGGTCGGAATAGTCCTGGACTTCAACTGGTACGAGGCTCTTACAAACTCACCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCTGCTGGTGGGAATTCAGCAACCGAACCTTACATAGTTGCTCATAATTTTCTCTTGGCACATGCTACTGCAGTTGCAAGATACCGTACGAAATATCAGgtatttccatcttgagaacctcagaagttcctctgaaaaataacatcactctagcactcctaggagtggtaaactgatgttattttattcaatgaagtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA