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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAATCTCGGCACCGTCGCCCCCCTTTCTCTCTCGCTCAAAAGTTGCTGCTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctctctcttatcgtacgtgatggatagcagtaactgatccggtgcgttgtacgatctgcggccgcttcgcttgcccctaccccgcacccgctcc...

Basic information

species Zea mays
transcript GRMZM2G008216_T03
intron # 1
splice site 5'
intron type U2

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|211064651|gb|FL344071.1|FL344071
EST:     CCGACCACCAACCATGGATGAGGCGCAAG                         TKGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211029655|gb|FL160177.1|FL160177
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211307979|gb|FL325109.1|FL325109
EST:     CCGACCCCCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211027219|gb|FL160172.1|FL160172
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|14202574|gb|BG836251.1|BG836251
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211098107|gb|FL309374.1|FL309374
EST:     CTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211277751|gb|FL328165.1|FL328165
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211456970|gb|FL307881.1|FL307881
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211155636|gb|FL334261.1|FL334261
EST:     TCTCCGACCACCAACCATGGATGAGGCGCAMG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: TCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211296213|gb|FL367911.1|FL367911
EST:     CTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211531451|gb|FL327591.1|FL327591
EST:     CTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|32912522|gb|CF017334.1|CF017334
EST:     GACCCCCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: GACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211027221|gb|FL160174.1|FL160174
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|32919706|gb|CF024518.1|CF024518
EST:     CTGGAGCCATCTCCCCTCTCTCCGACCCCCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211327340|gb|FL364058.1|FL364058
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|32919530|gb|CF024342.1|CF024342
EST:     GACCCCCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: GACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211031209|gb|FL344489.1|FL344489
EST:     TCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: TCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211056302|gb|FL363850.1|FL363850
EST:     AACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: AACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211416918|gb|FL328810.1|FL328810
EST:     CTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTCCTGGTT
genomic: CTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211027216|gb|FL160169.1|FL160169
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTKCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211337664|gb|FL335752.1|FL335752
EST:     CTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211105517|gb|FL308951.1|FL308951
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211520559|gb|FL367148.1|FL367148
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211528169|gb|FL316556.1|FL316556
EST:     CTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211103564|gb|FL331642.1|FL331642
EST:     CTGGAGCCCTCTCCCCTCTCTCTGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211027218|gb|FL160171.1|FL160171
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211152887|gb|FL357748.1|FL357748
EST:     CTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|60356864|gb|DN223837.1|DN223837
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211492114|gb|FL334538.1|FL334538
EST:     CCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211027220|gb|FL160173.1|FL160173
EST:     CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211375427|gb|FL332804.1|FL332804
EST:     CTCCGACCACCAACCATGGATGAKGCGCAAG                         TTGTGGAGTCAAAKGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
EST: gi|211029654|gb|FL160176.1|FL160176
EST:     CTGGAGCYCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAG                         TTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT
genomic: CTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTT

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: 150

AGGAATCTCGGCACCGTCGCCCCCCTTTCTCTCTCGCTCAAAAGTTGCTGCTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTTATCAGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

AGGAATCTCGGCACCGTCGCCCCCCTTTCTCTCTCGCTCAAAAGTTGCTGCTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTTATCAGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 127

AGGAATCTCGGCACCGTCGCCCCCCTTTCTCTCTCGCTCAAAAGTTGCTGCTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTTATCAGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

AGGAATCTCGGCACCGTCGCCCCCCTTTCTCTCTCGCTCAAAAGTTGCTGCTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctct ... cctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTTATCAGGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAATCTCGGCACCGTCGCCCCCCTTTCTCTCTCGCTCAAAAGTTGCTGCTGGAGCCCTCTCCCCTCTCTCCGACCACCAACCATGGATGAGGCGCAAGgtacgtctctctcttatcgtacgtgatggatagcagtaactgatccggtgcgttgtacgatctgcggccgcttcgcttgcccctaccccgcacccgctcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctacccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacccgc