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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtgtttgattaaagcactccttgatactttacccgctgcgtcgctttcctctcttttctctctctcatttatttggctgaaaggcttgatatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGACCCGTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG

Basic information

species Zea mays
transcript GRMZM2G031204_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031204_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g68710.1 (Oryza sativa), 3'ss of exon 3
----------cgtgtttgattaaagcactccttgatactttacccgctgcgtcgctttcctctcttttctctctctcatttatttggctgaaaggcttgata-tgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGACCCGTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG
            ||||  |  |||  |     || |||||| |    ||| | | ||        ||||    | ||  | |||  | ||||| | |||||| ||||||||||| |||||||||| |||||||| ||||||||| ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
ctcttttacaactgttaaagaaaaaaaaattgtggtactttcc----tgcatagttta-------tttccacatttccatcattgagttgaaatggttgataatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGACCCCTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG
















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|211236506|gb|FL293611.1|FL293611
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211132103|gb|FL293587.1|FL293587
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211132106|gb|FL293590.1|FL293590
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211133032|gb|FL293601.1|FL293601
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211133030|gb|FL293599.1|FL293599
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211133037|gb|FL293606.1|FL293606
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211240986|gb|FL293644.1|FL293644
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211236509|gb|FL293614.1|FL293614
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211133028|gb|FL293597.1|FL293597
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|23357637|gb|BU645286.1|BU645286
EST:     CATGTACCCTGCAAGCACACAAAGGAGACAAAATTAAGGGTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211238739|gb|FL293623.1|FL293623
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211238747|gb|FL293631.1|FL293631
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211236504|gb|FL293609.1|FL293609
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211240992|gb|FL293650.1|FL293650
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|108952959|gb|EC364521.1|EC364521
EST:     CATGTACCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC
EST: gi|211238746|gb|FL293630.1|FL293630
EST:     CATGTATCCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCATTATCGT                         GGGGCACTCACTGACGGATCAGTTTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGAC

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: 205

TACAAACCGGAGTCATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGACCCGTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

TACAAACCGGAGTCATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGACCCGTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

TACAAACCGGAGTCATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGACCCGTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

TACAAACCGGAGTCATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatct ... tatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGACCCGTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctctcttttctctctctcatttatttggctgaaaggcttgatatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGACCCGTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG
                                       gcttgat  putative branch site (score: 144)
                    tcatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtgtttgattaaagcactccttgatactttacccgctgcgtcgctttcctctcttttctctctctcatttatttggctgaaaggcttgatatgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGACCCGTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG

-gtgtttg
- - - - - - - gcactcc
- - - - - - - - - - - tgatact
- - - - - - - - - - - - - - - - -ccgctgc