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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCGCTGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatcttctactctgcttccaccccgcacggtgaggatcttgttagcattgacatgacggtggctgcttacgcgcgggaacaagctgtataaatcg...

Basic information

species Zea mays
transcript GRMZM2G160458_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160458_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 5'ss of exon 2
TGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCGCTGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatcttc---tactctgcttccaccccgcacggtgaggatcttgttagcattgacatgacggtggctgcttacgcgcgggaacaagctgtataaatcg
 || |||||||||||||||||||||||||||||||||||||| || ||||| |||||||| || |||||||||| ||||||||||||||| |||||||||||||| || | |   ||  ||||| | | | |     |       | |   | | ||||   |  | ||| ||| | |  |   | | ||||  |  ||   |
CGCCAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGCAATGCGCTCAACGAGCTGCTCGAGCTCAGGAACTGCTCCAGCTGCCTCTTCTTCGAGgtatatatttacacatatactgctacgatctcaagttgcttcaggcct--catctttgatgcgctgatggttgcgtgcttgataggagaagc-atgcaatagg
















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|71429209|gb|DR810259.1|DR810259
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|148946148|gb|EC891442.2|EC891442
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|148996317|gb|EE035601.2|EE035601
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|211395866|gb|FL418052.1|FL418052
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTAACCTT
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTA-CCTT
EST: gi|50323762|gb|CO518888.1|CO518888
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|211153699|gb|FL418636.1|FL418636
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|211049012|gb|FL423466.1|FL423466
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAANACAGAACGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|211130983|gb|FL371912.1|FL371912
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAA
EST: gi|211364314|gb|FL429339.1|FL429339
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|211491477|gb|FL425970.1|FL425970
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGG
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGG
EST: gi|71301915|gb|DR787034.1|DR787034
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|50326773|gb|CO521899.1|CO521899
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|211527534|gb|FL409937.1|FL409937
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTT
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTT
EST: gi|78089924|gb|DV518298.1|DV518298
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|9952850|gb|BE639433.1|BE639433
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|71429926|gb|DR810976.1|DR810976
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|148939576|gb|EC884188.2|EC884188
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|211204300|gb|FL385169.1|FL385169
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|211204896|gb|FL411811.1|FL411811
EST:     TGAACGMGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|211002651|gb|FL371731.1|FL371731
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|149070866|gb|EE159275.2|EE159275
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|32842309|gb|CD981990.1|CD981990
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGTCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|50332851|gb|CO527977.1|CO527977
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|71426064|gb|DR807114.1|DR807114
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
EST: gi|33468120|gb|CF245169.1|CF245169
EST:     TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAG                         TGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA
genomic: TGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGA

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: 317

TGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCGCTGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGACCATCAGTAAAATTTCTAGTTAATGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 117

TGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCGCTGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGACCATCAGTAAAATTTCTAGTTAATGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

TGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCGCTGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGACCATCAGTAAAATTTCTAGTTAATGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 100

TGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCGCTGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatct ... tgtattacagTGCAGAAAACAGAAGGATCTTTACCTTTGGATGGTGAAGTCTCCTGGAGGACCATCAGTAAAATTTCTAGTTAATGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCGCTGAACGAGCTCCTTGAGCTCAGGAGCTGCTCCAGCTGCCTTTTCTTCGAGgtatagatcttctactctgcttccaccccgcacggtgaggatcttgttagcattgacatgacggtggctgcttacgcgcgggaacaagctgtataaatcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacccc