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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGTGGATAGCCCTTTTGGACGGTTGGGGCTTACTGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacacattctaatatacttcacacagtcaatatgattcattatattggatgccctcctatcatagaaagtgtagagcagatgtatattttgtgatcctgtcttaattttgtctcatag

Basic information

species Zea mays
transcript GRMZM2G145578_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145578_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g31830.1 (Oryza sativa), 5'ss of exon 5
TGCTGTGGATAGCCCTTTTGGACGGTTGGGGCTTACTGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacacattctaatatactt-cacacagtcaatatgatt-cattatattgg--atgccc-tcctatcatagaa-agtgtagagcagatgtatattttgtgatcctgtcttaattttgtctcatag------------
||| |||||||| |||||||||||  | ||||||||||||||||||||||||||||| ||||||||||| |||  |||||| |||||||||||||| ||||| || |   ||   | ||||||  || |   |     ||||| | ||||  |    || ||  || ||||   ||  |  |   ||  ||  |  || ||||  ||| || ||  | |  | |   ||            
TGCAGTGGATAGTCCTTTTGGACGACTTGGGCTTACTGTTTGCTATGATTTGAGATTTCCAGAGCTTTACCAATGTTTGCGCTTTAAGCATCAAGCTCAGgtagtgatttatggcattatactgacataagtttttcctgattgccttatcctaagcatacctgtcatatctctgaggaaagctcaggtgaattgcatattgttttccagtattcttctaatatgccagtgacctttttag

upper sequence: GRMZM2G145578_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G38690.1 (Glycine max), 5'ss of exon 7
TGCTGTGGATAGCCCTTTTGGACGGTTGGGGCTTACTGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggt---tacacattctaatatacttcacacagtcaatatgattcattatattggatgccctcctatcatagaaagtgtagagcagatgtatattttgtgatcctgtcttaattttgtctcatag
||| || || || ||| ||||||| ||||| || | ||||||||||||||||||||| |||||| | || ||| |  | |||||  | ||| ||||||||||  |   |  | ||  || | | || |  | | |   |    |  |  || |    |   ||  | |  || ||  |  ||                                            
TGCAGTAGACAGTCCTATTGGACGTTTGGGCCTCAGTGTTTGCTATGATTTGAGATTTCCAGAGATGTACCAATTGCTACGTTTCCAACATGAAGCACAGgtaataagtggaaatattactttcctgcttaaaatgggtt--gtctacaatctaaatttttcttgtgttttacaacatccag--------------------------------------------

upper sequence: GRMZM2G145578_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv13s0067g03530.t01 (Vitis vinifera), 5'ss of exon 5
TGCTGTGGATAGCCCTTTTGGACGGTTGGGGCTTACTGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacacatt--ctaatatacttcacacagtcaatatgattcattatattggatgccctcctatcatagaaagtgtagagcagatgtatattttgtgatcctgtcttaattttgtctcatag
||| || || |||||  |||| || |||||  | || |||||||||||||||||||||||||||||||||||     |  | ||    ||  | ||||||||   ||||       |  |   |||  ||  ||  |   | ||  || | ||   |    |   ||     ||| | |  ||                                          
TGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAGCAGCTAAGGTTCCTACACGATGCACAGgtacatacaaggggattccttagctttgcattgt-gaccggctttcttttcttacctatgttaacattgattaaaatatgcag------------------------------------------

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|71773229|gb|DR971138.1|DR971138
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|93013637|gb|EB639157.1|EB639157
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|149099913|gb|EE185966.2|EE185966
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|211174534|gb|FL157623.1|FL157623
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATNACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|149099914|gb|EE185967.2|EE185967
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|32937778|gb|CF042597.1|CF042597
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|101385197|gb|EB814644.1|EB814644
EST:     TGAGATTCCCAGAGCTTTATCACATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGC
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGC
EST: gi|166537945|gb|EG311003.1|EG311003
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATC
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATC
EST: gi|67026709|gb|CO455458.1|CO455458
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|5296166|gb|AI783041.1|AI783041
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCGTTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|148930223|gb|EC872658.2|EC872658
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|211148755|gb|FL046692.1|FL046692
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|78078129|gb|DV506544.1|DV506544
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|71435450|gb|DR816500.1|DR816500
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|148928133|gb|EC872657.2|EC872657
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTCCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|60359149|gb|DN226122.1|DN226122
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|93013636|gb|EB639156.1|EB639156
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|76910593|gb|DV163937.1|DV163937
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|87152344|gb|DY397133.1|DY397133
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|78180385|gb|DV550758.1|DV550758
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGT
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGT
EST: gi|60346599|gb|DN213572.1|DN213572
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|211174535|gb|FL157624.1|FL157624
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|6695954|gb|AW289062.1|AW289062
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|211514747|gb|FL440709.1|FL440709
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATBTGCATTCACAAAGATAACGGGAGAGGCACMCTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|76016655|gb|DT943825.1|DT943825
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|71773228|gb|DR971137.1|DR971137
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|6127314|gb|AW129839.1|AW129839
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|78078128|gb|DV506543.1|DV506543
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|101385194|gb|EB814643.1|EB814643
EST:     CAAATTTTGGGTTTTAAGCATCAAGCACAG                         GTATTATTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: CAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|76294351|gb|DV033919.1|DV033919
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
EST: gi|12058143|gb|BF733058.1|BF733058
EST:     TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAG                         GTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG
genomic: TGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGG

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), 46 (downstream exon)
Score: 125

TGCTGTGGATAGCCCTTTTGGACGGTTGGGGCTTACTGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGGGAAATTCTCCTCCGAGCTCGTGCAATTGAGACACAATGTTAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 260

TGCTGTGGATAGCCCTTTTGGACGGTTGGGGCTTACTGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGGGAAATTCTCCTCCGAGCTCGTGCAATTGAGACACAATGTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 311

TGCTGTGGATAGCCCTTTTGGACGGTTGGGGCTTACTGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGGGAAATTCTCCTCCGAGCTCGTGCAATTGAGACACAATGTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

TGCTGTGGATAGCCCTTTTGGACGGTTGGGGCTTACTGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacac ... tgtctcatagGTATTACTAGTGCCATCTGCATTCACAAAGATAACGGGAGAGGCACACTGGGAAATTCTCCTCCGAGCTCGTGCAATTGAGACACAATGTTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGTGGATAGCCCTTTTGGACGGTTGGGGCTTACTGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAAGCATCAAGCACAGgtggttacacattctaatatacttcacacagtcaatatgattcattatattggatgccctcctatcatagaaagtgtagagcagatgtatattttgtgatcctgtcttaattttgtctcatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT