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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatctatgttgtggagttgctcagtataacagttcaactgatgtaatgcgtggttgatgtgttattctgtcctcaaatcagtgcacgtttgatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTAGATGAG

Basic information

species Zea mays
transcript GRMZM2G020040_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020040_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g48110.1 (Oryza sativa), 3'ss of exon 10
-tatctatgttgtggagttgctcagtataacagttcaactgatgtaatgcgtggttgatgtgttattctgtcctcaaatcagtgcacgtttgatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTAGATGAG
 |||||||   |  ||      || | |    |||   ||| |  | | | || ||| |||| || ||| | ||||  |         | || | || ||||||||||||||||||||  | |||||||| ||||| ||  ||||||| |||||||||
gtatctatacagaaga-ccaaacaatgtttttgtt--gctgctcaacttcatgattgttgtgctactctattctcatctgtaacactttctggtcttgcagATTGTTAAGAACTGGGACTCGAACAAACCGTGGCTTCCAAAAAAGAGGGTAGATGAG
















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|211482066|gb|FL394839.1|FL394839
EST:     GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAG                         ATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCTCAAAAGAGAGTA
genomic: GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTA
EST: gi|5901244|gb|AW042344.1|AW042344
EST:     GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTTCAAAAG                         ATTGTCAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTA
genomic: GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTA
EST: gi|32932694|gb|CF037506.1|CF037506
EST:     GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAG                         ATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCTCAAAAGAGAGTA
genomic: GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTA
EST: gi|211109353|gb|FL402583.1|FL402583
EST:     AACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAG                         ATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTA
genomic: AACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTA
EST: gi|32932673|gb|CF037485.1|CF037485
EST:     GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAG                         ATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCTCAAAAGAGAGTA
genomic: GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTA
EST: gi|211021977|gb|FL373955.1|FL373955
EST:     GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAG                         ATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCTCAAAAGAGAGTA
genomic: GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTA
EST: gi|26557797|gb|CA830032.1|CA830032
EST:     GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAG                         ATTGTTAAGAACTGGGAGACAAAC
genomic: GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAAC
EST: gi|116828779|gb|EC861048.1|EC861048
EST:     GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTTCAAAAG                         ATTGTCAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTA
genomic: GACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 87

ATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTAGATGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 116

ATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTAGATGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 111

ATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTAGATGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 239

ATTGAATGAATTAAAAACCCGACCAACGGCCTGTGAAAATGCTCGATTGTATCTTGATGAGCTGCAAAAGgtatcaataa ... gatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTAGATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcgtggttgatgtgttattctgtcctcaaatcagtgcacgtttgatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTAGATGAG
                                         gtttgat  putative branch site (score: 239)
                                               tttttc  CT-rich tract
                                          tttgattttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatctatgttgtggagttgctcagtataacagttcaactgatgtaatgcgtggttgatgtgttattctgtcctcaaatcagtgcacgtttgatttttcagATTGTTAAGAACTGGGAGACAAACAAACCATGGCTCCCCCAAAAGAGAGTAGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - -atgttgt
- - - - - - - -gttgctc
- - - - - - - - - - - - - - - - - - -ctgatgt
- - - - - - - - - - - - - - - - - - - - - - -atgcgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcacg