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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGAATTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagttctattttaagtgtattatagctacaataggctgcttttgaccaaaatttggtttcttttcag

Basic information

species Zea mays
transcript GRMZM2G028535_T02
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028535_T02 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 5'ss of exon 16
AGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGAATTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagttctattttaagtgtattatagctacaataggctgcttttgaccaaaatttggtttcttttcag------------------------------------------------------------------------
||||||| ||||||| ||||||||||| |||||||||||||||  |||||||||||||||||||||||||||| || || || |||||||| ||||||||||| | |  || | |    | | |||  |    ||  |    |  ||||    |  ||   |||| | | |                                                                          
AGGTAGATTCATTTCATCATGAGTATAACTCAATGGCATGCACCCTCGAATTTGTTGATGATGTGCAGTCAGCAATTGACCATATAAATCGCTATGGAAGgtatgcagtttttctccatactatatcctcatcacttt----ttttttttggaagtatgcagtttttctccttactatatccccatcatttcttttttttttttttgaactaaacttgattgtgttaaatatatgttcatttcag

upper sequence: GRMZM2G028535_T02 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA18G03830.1 (Glycine max), 5'ss of exon 16
AGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGAATTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt-tctattttaagtgtat-tatagctacaataggctgcttttgaccaa--aatttggtttcttttcag-----------------------------------------------
                             ||  ||||||||||||| ||| |||| ||||||||  |  ||||||| ||||| ||||||| |||||||||| | |  | | | |||||   |   || | | |  |  |||   | ||||   |||   |||| | | | |   |                                                 
---------------------------ATTCGTTGGCATGCACAGTTGAAATTGTGGATGATGTTTATGCAGCTATTGATCATATAAATCTTTATGGAAGGCATGCCACTCTTTATTTCTTGATAATgtgttggaagcatattttcctttcatccatctaattagatctgtagccgtgctgtaggcttagattgaaatttttcacattttctcctttgtggcag
















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|61118748|gb|DN559709.1|DN559709
EST:     TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAG                         TGCACACACAGACTGCATCATCACAACTGATAAAAGTGCTGCAAAGGCCTT
genomic: TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt ... ttcttttcagTGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT
EST: gi|60344250|gb|DN211223.1|DN211223
EST:     TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAG                         TGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT
genomic: TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt ... ttcttttcagTGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT
EST: gi|60355192|gb|DN222165.1|DN222165
EST:     TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAG                         TGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT
genomic: TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt ... ttcttttcagTGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT
EST: gi|211181077|gb|FL441225.1|FL441225
EST:     TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAG                         TGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT
genomic: TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt ... ttcttttcagTGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT
EST: gi|101391685|gb|EB817779.1|EB817779
EST:     TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAG                         TGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT
genomic: TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt ... ttcttttcagTGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT
EST: gi|149066719|gb|EE286860.2|EE286860
EST:     TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAG                         TGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT
genomic: TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt ... ttcttttcagTGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT
EST: gi|67017479|gb|CO446228.1|CO446228
EST:     TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAG                         TGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCGGAGGCCTT
genomic: TTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt ... ttcttttcagTGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTT

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: 180

AGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGAATTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt ... ttcttttcagTGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG


Block sizes: 46 (upstream exon), 41 (downstream exon)
Score: 4

AGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGAATTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt ... ttcttttcagTGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG


Block sizes: 45 (upstream exon), 20 (downstream exon)
Score: 6

AGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGAATTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt ... ttcttttcagTGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 638

AGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGAATTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagt ... ttcttttcagTGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGAATTTGTTGATGATGTGCAGTCAGCTATCGATCACATAAATCGTTATGGAAGgtaaggaagttctattttaagtgtattatagctacaataggctgcttttgaccaaaatttggtttcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG