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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGCATGCTAGTGGCAATGCGAAAGTTGGCATTGATCTGGAGGAAGGCGCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagtatgaacagtaggttagaacaacagtgttgggttttcaaacttttttgtggtaattgaacatgtgctcattgggtatggaaaatgttcgca...

Basic information

species Zea mays
transcript GRMZM2G381744_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381744_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 5'ss of exon 11
CTGAGCATGCTAGTGGCAATGCGAAAGTTGGCATTGATCTGGAGGAAGGCGCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcag----tatga----acagtaggttagaacaa-------cagtgttgggttttcaaacttttttgtggtaattg-aacatgtgctcattgggtatggaaaatgttcgca------------------------------------------------------------------
|||| |||||| |||| ||| |||||||||| |||||  |||| ||||| |  ||||||||  |||| |   | |||||||||||||| ||||| |||||||||||||      || |     ||||| |  | || |         | |||  ||    ||  || |||| |  |  | |  | |       |||   | |    | | || |||                                                                  
CTGAACATGCTGGTGGGAATACGAAAGTTGGTATTGACTTGGAAGAAGGTGGTTGCAAGGATGTCTCAATCATGAAAATATGGGACCTTTATGTTACAAAgtaagtcatatgccataaccttccagtatggcataataggtgcacgtactgtatgggaagcacgctgttttttacttttcgtgatacccatgtattcattttttttattatttgcatgtttactggcgagacttaagcaagttggccaacctcatatcatgtgtgttcttttctctcatcag
















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|211324907|gb|FL462770.1|FL462770
EST:     GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAA                         GTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
genomic: GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
EST: gi|9824878|gb|BE574975.1|BE574975
EST:     GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAA                         GTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
genomic: GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
EST: gi|33095218|gb|CF055212.1|CF055212
EST:     AAAAATATGGGACCTCTATGTCACAAA                         GTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
genomic: AAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
EST: gi|32919902|gb|CF024714.1|CF024714
EST:     GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAA                         GTCTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
genomic: GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
EST: gi|5770240|gb|AI973414.1|AI973414
EST:     GCCTGCAAGGACATCTCGACTTTAAAAATATGGGGCCTCTATGTCNCAAA                         GTTTTTTGCCCTAAAA
genomic: GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAA
EST: gi|110540574|gb|EE044494.1|EE044494
EST:     GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAA                         GTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
genomic: GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
EST: gi|32919903|gb|CF024715.1|CF024715
EST:     GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAA                         GTCTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
genomic: GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
EST: gi|211389515|gb|FL138775.1|FL138775
EST:     TATGTCACAAA                         GTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
genomic: TATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
EST: gi|211335351|gb|FL444762.1|FL444762
EST:     TATGTCACAAA                         GTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
genomic: TATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
EST: gi|60349872|gb|DN216845.1|DN216845
EST:     GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAA                         GTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT
genomic: GCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGT

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: 146

CTGAGCATGCTAGTGGCAATGCGAAAGTTGGCATTGATCTGGAGGAAGGCGCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

CTGAGCATGCTAGTGGCAATGCGAAAGTTGGCATTGATCTGGAGGAAGGCGCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

CTGAGCATGCTAGTGGCAATGCGAAAGTTGGCATTGATCTGGAGGAAGGCGCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

CTGAGCATGCTAGTGGCAATGCGAAAGTTGGCATTGATCTGGAGGAAGGCGCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagt ... tgccgtacagGTTTTTTGCCCTAAAATACTCTGCCGATGCTGCTTGCACGGTGCTGCGGGTTGACCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAGCATGCTAGTGGCAATGCGAAAGTTGGCATTGATCTGGAGGAAGGCGCCTGCAAGGACATCTCGACTTTAAAAATATGGGACCTCTATGTCACAAAgtaagtcagtatgaacagtaggttagaacaacagtgttgggttttcaaacttttttgtggtaattgaacatgtgctcattgggtatggaaaatgttcgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atggaaaa