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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaatggatatatttttttaatatacatgatgtttgtgccaactgtgaagtgtcctacattaaaacacagtattgattttgttgattcctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG

Basic information

species Zea mays
transcript GRMZM5G856653_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856653_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g53930.2 (Oryza sativa), 3'ss of exon 3
agaaaatggatatatttttttaatatacatgatgtttgtgccaactgtgaagtgtcctacattaaaacacagtattgattttgttgattcctgtgagc--agGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG
    ||   | || |    | || |      || | | |   || | |  | |||  | |    ||      | |  |   |  ||||| |||||| |  |||| || ||||||||||||||||||||||| ||||| ||||||||||| || ||||||||||||||| ||||||| 
-ctcaagacaaatgtggcatcaacac-tgcaatatcttttttaattttataatgttatgcccataattttgatgtatagactaatgatttctgtgaactcagGTGGGGGAAGATGTTGTGGCTGAATTGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTT
















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|148957702|gb|EC903823.2|EC903823
EST:     CATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACG                         GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGT
genomic: CATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACGgtaaaaacaa ... ctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGT
EST: gi|211232468|gb|FK968372.1|FK968372
EST:     CATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACG                         GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGT
genomic: CATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACGgtaaaaacaa ... ctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGT
EST: gi|148980000|gb|EE026913.2|EE026913
EST:     CATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACG                         GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGT
genomic: CATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACGgtaaaaacaa ... ctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGT
EST: gi|148933666|gb|EC877560.2|EC877560
EST:     CATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACG                         GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGT
genomic: CATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACGgtaaaaacaa ... ctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGT
EST: gi|211232471|gb|FK968375.1|FK968375
EST:     CATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACG                         GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGT
genomic: CATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACGgtaaaaacaa ... ctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGT

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: 161

GAGGGAACTGGGTTTCACCTTTTCTTTCCCAGTGCACCAAACATCTATATCATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACGgtaaaaacaa ... ctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 291

GAGGGAACTGGGTTTCACCTTTTCTTTCCCAGTGCACCAAACATCTATATCATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACGgtaaaaacaa ... ctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

GAGGGAACTGGGTTTCACCTTTTCTTTCCCAGTGCACCAAACATCTATATCATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACGgtaaaaacaa ... ctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

GAGGGAACTGGGTTTCACCTTTTCTTTCCCAGTGCACCAAACATCTATATCATCGGGGACTCTAATTAAGTGGACCAAAGGATTTTGCATCAATGGCACGgtaaaaacaa ... ctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaagtgtcctacattaaaacacagtattgattttgttgattcctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG
                                          ttcctgt  CT-rich tract
            tacattaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaaatggatatatttttttaatatacatgatgtttgtgccaactgtgaagtgtcctacattaaaacacagtattgattttgttgattcctgtgagcagGTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - atacatg
- - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cctacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaca