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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctgttcaattaagaaaaataattaaacgctacacagcttacatttaagcatcatggttggctgatatgttttactcttgaacgatag

Basic information

species Zea mays
transcript GRMZM2G002687_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002687_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g35570.3 (Oryza sativa), 5'ss of exon 4
TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctgt---tcaattaagaaaaat-------aattaaacgc-----tacaca---gcttacatttaagcatcatggttggctgatatgttttactcttgaacgatag
||||||||||||||||||| |  |||||||||||||||| ||    |||||||| ||   | |   | | |  || || ||       | |  | |||     |||      | || |||  || |||  |  || ||||||||  ||||||||||||||| ||
TGCTTTTTATGAAAACATGGTTAAAGTTGCCAGATGTGTGACATATAATAAGgtgagcagtttaagttagtctagcaatattttgggcagtggatcgcttggttacttgcttgtttgcatccaaccattgtcttttgctgatattgtttactcttgaacgacag
















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|67015552|gb|CO444301.1|CO444301
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATANNGAAAG-TTAG
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAG-GAAAGGTTAG
EST: gi|148959767|gb|EC905658.2|EC905658
EST:     CTTTTTATGATAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
EST: gi|67037924|gb|CO464466.1|CO464466
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTNCA-TCTTGAGGATCACATAGGAAAGGTTAG
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTT-CAATCTTGAGGATCACATAGGAAAGGTTAG
EST: gi|6020814|gb|AW065742.1|AW065742
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
EST: gi|149010069|gb|EE041876.2|EE041876
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAGAGGTTAGC
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
EST: gi|71305908|gb|DR789081.1|DR789081
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTCAATCTTGAGGATCA
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCA
EST: gi|149105517|gb|EE291042.2|EE291042
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGT
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGT
EST: gi|9953035|gb|BE639618.1|BE639618
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
EST: gi|91049846|gb|EB160264.1|EB160264
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
EST: gi|211139771|gb|FL315903.1|FL315903
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
EST: gi|149073834|gb|EE162156.2|EE162156
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTNCA-TCTTGAGGATCACATAGGAAAGGTTAG
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTT-CAATCTTGAGGATCACATAGGAAAGGTTAG
EST: gi|67014073|gb|CO442822.1|CO442822
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
EST: gi|148973279|gb|EE024361.2|EE024361
EST:     CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG                         GCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC
genomic: CTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGC

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: 48 (upstream exon), 47 (downstream exon)
Score: 124

TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGCTTTCCTCCAGTGCAGGCAGTCCCATCATTCCCTTCTTCATTTCCCCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGCTTTCCTCCAGTGCAGGCAGTCCCATCATTCCCTTCTTCATTTCCCCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGCTTTCCTCCAGTGCAGGCAGTCCCATCATTCCCTTCTTCATTTCCCCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctg ... tgaacgatagGCTATTGGAATATTTGGGTTCAATCTTGAGGATCACATAGGAAAGGTTAGCTTTCCTCCAGTGCAGGCAGTCCCATCATTCCCTTCTTCATTTCCCCATC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAGgtaagagctgttcaattaagaaaaataattaaacgctacacagcttacatttaagcatcatggttggctgatatgttttactcttgaacgatag

- - - - - - - - - - - - - - - CAGATG