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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaacttgtgcctgtttaccattgttcttcagggagttctttctatcattgaaattctatattttaacattttaatgatttgttcttatgcag

Basic information

species Zea mays
transcript GRMZM2G082664_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os06g30460.4 (Oryza sativa), 5'ss of exon 14
GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaac-ttgtgcctgtttaccattgttcttcagggagttctttctatcattgaaattctatattttaacattttaatgatttgttcttatgcag
||||||||| |||||||||||||| | |||||||||||||| ||||| |||||||| || || ||||||||||| |  |  || | ||  |||  ||||| | ||  |  |     | ||    ||||       ||||| ||  |||| |    |||  ||| |||||
GTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAGgcatgtgatattttacccttttgtcattgcttttgggaaatcctgtactgctgttga-------tatttgaatgttttgaca--ttg--cttctgcag

upper sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 16
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 5'ss of exon 19
GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaacttgtgcctgtttaccattgttcttcagggagttctttctatcattgaaattctatattttaacattttaatgatttgttcttatgcag
|| ||  |  | |||||||||||| |||| |||||||||   || || ||||||||||| ||||||||||||  |      |||       | ||| | |  | |    | || | ||| |  || |||      ||  |||  ||||  |  |||  |||||| |||
GTCAAAGAATTAGCTGAAAAGGCACGAGCAGGGAAGCTTAAGCCCAATGAATTTCAAGGAGGAACTTTCAGgtgaatg---tgtcttataattccagtatgatactattacttgtgtcttttgttaaaagcagccatcataattttttttttttttaatcttatacag
















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|71433813|gb|DR814863.1|DR814863
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|61119124|gb|DN560085.1|DN560085
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|211174833|gb|FL413958.1|FL413958
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACMCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|76924990|gb|DV170231.1|DV170231
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|60347222|gb|DN214195.1|DN214195
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGGACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|149003161|gb|EE038899.2|EE038899
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|47961688|gb|CN844397.1|CN844397
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|50331519|gb|CO526645.1|CO526645
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|37398003|gb|CF636310.1|CF636310
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|40337298|gb|CK371368.1|CK371368
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|50331482|gb|CO526608.1|CO526608
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|50331481|gb|CO526607.1|CO526607
EST:     CTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: CTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|91053971|gb|EB164389.1|EB164389
EST:     TTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: TTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
EST: gi|88758153|gb|DY542294.1|DY542294
EST:     GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAG                         TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA
genomic: GCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAA

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: 113

GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 186

GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 202

GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaact ... tcttatgcagTATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaacttgtgcctgtttaccattgttcttcagggagttctttctatcattgaaattctatattttaacattttaatgatttgttcttatgcag

- - - - - - - - - -  GCAAGA
- - - - - - - - - - - - AGAGCT