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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactgtgtactactgaataatacctgcagcatctggaacaactgggacataccttattgtgtttctgtaacacaagcgcttccaatattgtttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACGCTGGTCCAGACCTTCGGACAGAAGAACCATGTCTGCCTCAAGGACGGGT

Basic information

species Zea mays
transcript GRMZM5G898668_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G898668_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 2
--tactgtgtactactgaataatacctgcagcatctggaacaactgggacataccttattgtgtttctgtaacacaa-gcgcttccaatattgttttt--ttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACGCTGGTCCAGACCTTCGGACAGAAGAACCATGTCTGCCTCAAGGACGGGT
   |   | |||  |||| |   |||| |    | |   ||     |  || |   | ||  |||  |  | |  |  |  |||    |  |||| ||  |||||||||| || || || ||||| || ||||| || ||||| ||||||||||| ||||| |||||||| ||||| ||||||||||||||| | |||||||| |
ttaatcatctacc-ctgattggcaccttc----tatcatactttgtgcccacattctctttggttatttcagcgtattgatcttttgcttctgttattgtttcagGAAGAAAAGGCAATTGGACGTGGAATCCTCCCATTGCTTCAGCGTGCCACCCTGGTTCAGACCTTTGGACAAAAGAACCATGTCTGCTTGAAGGACGGCT
















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|149100129|gb|EE186184.2|EE186184
EST:     ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAG                         GAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
genomic: ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
EST: gi|91049522|gb|EB159940.1|EB159940
EST:     ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAG                         GAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
genomic: ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
EST: gi|71421490|gb|DR805460.1|DR805460
EST:     ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAG                         GAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
genomic: ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
EST: gi|78087615|gb|DV516008.1|DV516008
EST:     ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAG                         GAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
genomic: ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
EST: gi|71325429|gb|DR799400.1|DR799400
EST:     ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAG                         GAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
genomic: ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
EST: gi|149021734|gb|EE045807.2|EE045807
EST:     ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAG                         GAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
genomic: ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
EST: gi|93012105|gb|EB637625.1|EB637625
EST:     ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAG                         GAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
genomic: ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
EST: gi|148954400|gb|EC899817.2|EC899817
EST:     ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAG                         GAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG
genomic: ACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACG

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: 26 (upstream exon), 24 (downstream exon)
Score: 2

CGAGCTCGTCGCCACCAACTGGCCGTACTGGAACAGGTCGGAGGGCGCCGACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACGCTGGTCCAGACCTTCGGACAGAAGAACCATGTCTGCCTCAAGGACGGGT


Block sizes: 40 (upstream exon), 34 (downstream exon)
Score: 14

CGAGCTCGTCGCCACCAACTGGCCGTACTGGAACAGGTCGGAGGGCGCCGACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACGCTGGTCCAGACCTTCGGACAGAAGAACCATGTCTGCCTCAAGGACGGGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 29

CGAGCTCGTCGCCACCAACTGGCCGTACTGGAACAGGTCGGAGGGCGCCGACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACGCTGGTCCAGACCTTCGGACAGAAGAACCATGTCTGCCTCAAGGACGGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

CGAGCTCGTCGCCACCAACTGGCCGTACTGGAACAGGTCGGAGGGCGCCGACCACTTCTTCGTCACGCCACATGACTTTGGCGCTTGCTTCCATTATCAGgtaggtagtt ... tttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACGCTGGTCCAGACCTTCGGACAGAAGAACCATGTCTGCCTCAAGGACGGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacataccttattgtgtttctgtaacacaagcgcttccaatattgtttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACGCTGGTCCAGACCTTCGGACAGAAGAACCATGTCTGCCTCAAGGACGGGT
                   ctgtaac  putative branch site (score: 165)
                                          ttgtttttttc  putative PPT
                                      aatattgtttttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactgtgtactactgaataatacctgcagcatctggaacaactgggacataccttattgtgtttctgtaacacaagcgcttccaatattgtttttttcagGAAGAGAAAGCGATCGGACGCGGGATCCTTCCCTTGCTCCAGCGTGCCACGCTGGTCCAGACCTTCGGACAGAAGAACCATGTCTGCCTCAAGGACGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
tactgtg
- - - - -ctactga
- - - - - - - - - - - -ctgcagc
- - - - - - - - - - - - - - - - - - aacaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttcca