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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTTAGTGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcagtatcccatggaacatgcaataatttcctctagtaaatatgttacaaaaacttcatattcaatttggaatattcaaatttcaaagtgattc...

Basic information

species Zea mays
transcript GRMZM5G825110_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 4
CAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTTAGTGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcagtatcccatggaacatgcaataatttcctctagtaaatatgttacaaaaacttcatattcaatttggaatattcaaa---tttcaaagtgattc
|||||||| || ||||||||||||||||||||  | |||||||| || ||||| || ||||||||||||||||| || || ||||||||||| ||||| |||| |  |||| | | ||  ||  || || |||  |   |  | || |  || ||     || | |   | |   ||||| | |     ||   |  ||||  
CAGCTTGTTAACACAGTAACTTCAGATCACTTATTGTATAAGGTTGTCAGTGGTCTCATAAAGTATCAGATGTTCATTTGCTATTTTCTTTACATTGCTGgtaagtacagtgtgcaatt-aatttgaaacaataactattcattaaga-atttcattgtgtttaaaaagactcaagaatagttatgtgtttcttacatgatc-
















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|71439838|gb|DR820888.1|DR820888
EST:     TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAG                         GTTTTGTATGGTTTATTTTGACTCTCAAGAAAA-GACATATAAGTACCAGT
genomic: TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
EST: gi|71426534|gb|DR807584.1|DR807584
EST:     TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAG                         GTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
genomic: TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
EST: gi|76287486|gb|DV027054.1|DV027054
EST:     TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAG                         GTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
genomic: TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
EST: gi|149000638|gb|EE037841.2|EE037841
EST:     TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAG                         GTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATACAAGTACCAGT
genomic: TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
EST: gi|71426083|gb|DR807133.1|DR807133
EST:     TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAG                         GTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
genomic: TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
EST: gi|93283949|gb|EB676213.1|EB676213
EST:     TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAG                         GTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
genomic: TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
EST: gi|76014867|gb|DT942037.1|DT942037
EST:     TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAG                         GTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
genomic: TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGT
EST: gi|78121241|gb|DV539625.1|DV539625
EST:     TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAG                         GTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACAT
genomic: TGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACAT

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), 45 (downstream exon)
Score: 79

CAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTTAGTGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGTTCAAACAGTATGCCTGGACGCACATGATACTTCTAACGGTTTTTGCACA


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

CAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTTAGTGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGTTCAAACAGTATGCCTGGACGCACATGATACTTCTAACGGTTTTTGCACA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 80

CAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTTAGTGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGTTCAAACAGTATGCCTGGACGCACATGATACTTCTAACGGTTTTTGCACA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 49

CAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTTAGTGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcag ... ttcgttccagGTTTTGTATGGTTTATTTTGACTCTCAAGAAAAAGACATATAAGTACCAGTTCAAACAGTATGCCTGGACGCACATGATACTTCTAACGGTTTTTGCACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTTAGTGGCCTAATAAAGTATCAGATGTTTATCTGTTATTTTCTTTATATTGCAGgtaggctcagtatcccatggaacatgcaataatttcctctagtaaatatgttacaaaaacttcatattcaatttggaatattcaaatttcaaagtgattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaaac