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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGTACTCTATGACGTGTTGCAAAAGGAGGTGGTTTCCTTGAGAAAGGCATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgctatactactattgcggaaattaagatgctactttatcatttagtaattggtactactcccggcttcctaaaatagatgaccttatagcatt...

Basic information

species Zea mays
transcript GRMZM5G832989_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G832989_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g50320.1 (Oryza sativa), 5'ss of exon 9
TGGTGTACTCTATGACGTGTTGCAAAAGGAGGTGGTTTCCTTGAGAAAGGCATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgctatactactattgcggaaattaagatgctactttatca-tttagtaattggtactactcccggcttcctaaaatagatgaccttatagcatt
|||||||||||||||| || |||||||||||||  |||| |||||||||||||||||||||||||| |||| |||||| ||||| || |||||||| ||||||||   ||| | | |   |     | |   |||   |    | || |   ||   |  | |   | |   || |||    |  |               
TGGTGTACTCTATGACATGCTGCAAAAGGAGGTCATTTCATTGAGAAAGGCATGCCATGAGAAAGATCAAAGTCTAAAAGACAAGGATGATGCAATTGAGgtatggcactagaattcctgttt---attatggatttaatgggaccaatgctgtgggtcatgcctttgctaactgcctcttgtttacag------------
















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|67015040|gb|CO443789.1|CO443789
EST:     CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAG                         ATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
genomic: CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
EST: gi|78544693|gb|DV622191.1|DV622191
EST:     CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAG                         ATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
genomic: CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
EST: gi|61119815|gb|DN560776.1|DN560776
EST:     CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAG                         ATGCTAGCAAAGAAAGTAGATACATTACATAAAGC
genomic: CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGC
EST: gi|31350085|gb|CD434442.1|CD434442
EST:     CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAG                         ATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
genomic: CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
EST: gi|166600902|gb|EG321320.1|EG321320
EST:     ATGCCATGAGAAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAG                         ATGCTAGCAAAGA
genomic: ATGCCATGAG-AAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGA
EST: gi|60400346|gb|DN233153.1|DN233153
EST:     CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAG                         ATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
genomic: CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
EST: gi|32934733|gb|CF039545.1|CF039545
EST:     CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAG                         ATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
genomic: CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
EST: gi|32934768|gb|CF039580.1|CF039580
EST:     CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAG                         ATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
genomic: CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
EST: gi|32934475|gb|CF039287.1|CF039287
EST:     CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAG                         ATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
genomic: CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
EST: gi|60356638|gb|DN223611.1|DN223611
EST:     CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAG                         ATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
genomic: CATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCT
EST: gi|67041884|gb|CO468139.1|CO468139
EST:     TGCCATGGAGAAAGACCAAACTCTAAGGGACAA-GAANGATGCA-TGGAG                         ATGCCTAGCAA-GAAAGTAGATACATTACCTAAGGCAA-GGAAGTGGA
genomic: TGCCATG-AGAAAGACCAAACTCTAAAGGACAAAGAA-GATGCAATGGAGgtatgatgct ... ttgcctacagATGC-TAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGA

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: 215

TGGTGTACTCTATGACGTGTTGCAAAAGGAGGTGGTTTCCTTGAGAAAGGCATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCTAAAAAGAAGAGGCAAGAGATAGCTGCTTTGGAGAAAAAATTTGCCGCGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 56

TGGTGTACTCTATGACGTGTTGCAAAAGGAGGTGGTTTCCTTGAGAAAGGCATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCTAAAAAGAAGAGGCAAGAGATAGCTGCTTTGGAGAAAAAATTTGCCGCGG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 38

TGGTGTACTCTATGACGTGTTGCAAAAGGAGGTGGTTTCCTTGAGAAAGGCATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCTAAAAAGAAGAGGCAAGAGATAGCTGCTTTGGAGAAAAAATTTGCCGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

TGGTGTACTCTATGACGTGTTGCAAAAGGAGGTGGTTTCCTTGAGAAAGGCATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgct ... ttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCTAAAAAGAAGAGGCAAGAGATAGCTGCTTTGGAGAAAAAATTTGCCGCGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGTACTCTATGACGTGTTGCAAAAGGAGGTGGTTTCCTTGAGAAAGGCATGCCATGAGAAAGACCAAACTCTAAAGGACAAAGAAGATGCAATGGAGgtatgatgctatactactattgcggaaattaagatgctactttatcatttagtaattggtactactcccggcttcctaaaatagatgaccttatagcatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataga