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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctcccaaaagtttaatgtcagggcatcaggtacactggtcaattggtgttattaacactgtttgttgctgcag

Basic information

species Zea mays
transcript GRMZM2G100620_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100620_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g15700.1 (Oryza sativa), 5'ss of exon 5
AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctcccaaaagtttaatgtcagggcatcaggtacactggtcaattggtgttattaacactgtttgttgctgcag
|||||| ||  ||||||||| | ||||||||| ||||||||||| ||||| ||||||||||| ||||  || |||||      |   ||   |||  ||  |||   |||| |  ||||| || |   | ||  ||||| | |||| || |||||
AAAGTCGAATCTTGGGATAAAAAGTATCAATATCTACTTTTTGCAGCAGAGCCCTATGAAATTATTGGCTTTAAGgtgtgtgttttgaatgttttgctgctaggatttcagatcaactggccattgtattttgctaacaatttttgctgttgcag
















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|60341101|gb|DN208074.1|DN208074
EST:     TCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: TCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|19351244|gb|BM895776.1|BM895776
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATNGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|149014483|gb|EE044106.2|EE044106
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|19272503|gb|BM888759.1|BM888759
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|149111001|gb|EE294500.2|EE294500
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|91056062|gb|EB166480.1|EB166480
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|18648819|gb|BM497638.1|BM497638
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|76292130|gb|DV031698.1|DV031698
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|148944813|gb|EC889958.2|EC889958
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|78092801|gb|DV521175.1|DV521175
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|78077143|gb|DV505577.1|DV505577
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|148937013|gb|EC881184.2|EC881184
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|71439882|gb|DR820932.1|DR820932
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|149111002|gb|EE294501.2|EE294501
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|18654690|gb|BM499495.1|BM499495
EST:     TTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: TTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|50330974|gb|CO526100.1|CO526100
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|78113433|gb|DV531825.1|DV531825
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|32863198|gb|CF002880.1|CF002880
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATT
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATT
EST: gi|6564142|gb|AW231764.1|AW231764
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|149081122|gb|EE170228.2|EE170228
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|19351666|gb|BM896198.1|BM896198
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|19351243|gb|BM895775.1|BM895775
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|32803496|gb|CD955732.1|CD955732
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|211028537|gb|FL445303.1|FL445303
EST:     TGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: TGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
EST: gi|166446380|gb|EG075576.1|EG075576
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGA
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGA
EST: gi|18648881|gb|BM497700.1|BM497700
EST:     ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG                         ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG
genomic: ATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGG

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: 269

AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctc ... gttgctgcagATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAGgtaatctctcccaaaagtttaatgtcagggcatcaggtacactggtcaattggtgttattaacactgtttgttgctgcag

- - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - -  CTGCAG