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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtattatgaattggcttttgcagttgcaccaaggcatggttttgtaaatactactacctccgttctcgaatatttgttgcccgctagttcatttttgaactaaaccacgacaaataaaaaagaatggagggagtactatataaactattggttgtactaaagcaaactttatatgcccaaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACTGTCACTGGAATCATTGAGGTTCTTGACAACACTACACTGAGGATCACTG

Basic information

species Zea mays
transcript GRMZM2G121210_T02
intron # 6
splice site 3'
intron type U2

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|211094724|gb|FL034696.1|FL034696
EST:     TGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAG                         GGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACT
genomic: TGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAGgttagtatta ... aaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACT
EST: gi|211094716|gb|FL034688.1|FL034688
EST:     TGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAG                         GGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACT
genomic: TGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAGgttagtatta ... aaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACT
EST: gi|211094715|gb|FL034687.1|FL034687
EST:     TGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAG                         GGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACT
genomic: TGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAGgttagtatta ... aaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACT
EST: gi|211097188|gb|FL034700.1|FL034700
EST:     TGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAG                         GGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACT
genomic: TGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAGgttagtatta ... aaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACT
EST: gi|31558543|gb|CD527755.1|CD527755
EST:     TGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAG                         GGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACT
genomic: TGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAGgttagtatta ... aaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACT

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: 786

TATTCCAAACTACAATCCAAGAGACATTCTTGCTAACCTCAGGCGATTGCTGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAGgttagtatta ... aaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACTGTCACTGGAATCATTGAGGTTCTTGACAACACTACACTGAGGATCACTG


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 72

TATTCCAAACTACAATCCAAGAGACATTCTTGCTAACCTCAGGCGATTGCTGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAGgttagtatta ... aaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACTGTCACTGGAATCATTGAGGTTCTTGACAACACTACACTGAGGATCACTG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 48

TATTCCAAACTACAATCCAAGAGACATTCTTGCTAACCTCAGGCGATTGCTGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAGgttagtatta ... aaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACTGTCACTGGAATCATTGAGGTTCTTGACAACACTACACTGAGGATCACTG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 31

TATTCCAAACTACAATCCAAGAGACATTCTTGCTAACCTCAGGCGATTGCTGAATGGAGAGTCTACTGTACCAATGCACCCATGGTACAGGGGATTTAAGgttagtatta ... aaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACTGTCACTGGAATCATTGAGGTTCTTGACAACACTACACTGAGGATCACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactatataaactattggttgtactaaagcaaactttatatgcccaaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACTGTCACTGGAATCATTGAGGTTCTTGACAACACTACACTGAGGATCACTG
                     tactaaa  putative branch site (score: 31)
     tataaactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtattatgaattggcttttgcagttgcaccaaggcatggttttgtaaatactactacctccgttctcgaatatttgttgcccgctagttcatttttgaactaaaccacgacaaataaaaaagaatggagggagtactatataaactattggttgtactaaagcaaactttatatgcccaaatttacagGGCTCTATAGAGAAGACAGTCAATACAAAGGTAGCTGGTTCCACATATACTGTCACTGGAATCATTGAGGTTCTTGACAACACTACACTGAGGATCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT