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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaatgttcaatatttcattcaaattaattttatatttcttgaatttttttgcttagatgtttctgtccgtttgaacctgtgcttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTG

Basic information

species Zea mays
transcript GRMZM2G029559_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 5
------------------------------------------------gtgagtaatgttcaatatttcattcaaattaattttatatt----tcttgaatttttttgcttagatgtttctgtccgtttgaacctgtgcttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTG
                                                |    ||   ||   | |||| ||||  || || ||  ||     | | | ||  || |   |   | |  | |  | ||  |     || || ||||||||||| |||||||||||||| |||||| | || |||||||||||||| |  | |||||| ||| | | ||||||| | || |||  ||| |||| |||||
gtgagtgatctttcataaatatttaggatcattcttgattattttccagctcctagaattttgtgtttctttcaggttgatctttcatagacatttaggatcattcttgattattttaccagctccttgaatttcttgtttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAATACTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTG

upper sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 4
gtgagtaatgttcaatatttcattcaaattaattttatatttcttgaatttttttgcttagatgtttctgtccgtttgaacctgtgcttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTG
||||||  | ||| |||  |  || | || |         ||||||| | ||||     |   | ||||         |   | || || || |||||||| || ||||||||||  |||||| | || |||||||||||||| |  |||||||| ||| | ||||||||  | ||  ||  |||||||| |||||
gtgagtggtcttccatagatatttaagatca---------ttcttgattatttt-----acgagcttctag------aattgtatgtttcttccagGCCCACATCGAGCAGTGGAATGACTTTTCGGCCACAGAGGTTGATGCTAATATTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTG
















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|211045449|gb|FL056742.1|FL056742
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|17921484|gb|BM259135.1|BM259135
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|15426721|gb|BI542543.1|BI542543
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|32823439|gb|CD963161.1|CD963161
EST:     GATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: GATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|17921811|gb|BM259462.1|BM259462
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|56382464|gb|CV985133.1|CV985133
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|33100592|gb|CF060552.1|CF060552
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|211045448|gb|FL056741.1|FL056741
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|21987889|gb|BQ779417.1|BQ779417
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGGGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|32942861|gb|CF047680.1|CF047680
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|32807718|gb|CD959952.1|CD959952
EST:     GATCTTCCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: GATCTT-CACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|211045450|gb|FL056743.1|FL056743
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|30087596|gb|CB885802.1|CB885802
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGCTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|32908341|gb|CF013154.1|CF013154
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|211045447|gb|FL056740.1|FL056740
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|26456546|gb|CA828129.1|CA828129
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|211045445|gb|FL056738.1|FL056738
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|20301474|gb|BQ164417.1|BQ164417
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|211045441|gb|FL056734.1|FL056734
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTT
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTT
EST: gi|31406016|gb|CD484748.1|CD484748
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|74237946|gb|DT645860.1|DT645860
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|33093176|gb|CF053170.1|CF053170
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|31359821|gb|CD444178.1|CD444178
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|21331579|gb|BQ486960.1|BQ486960
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|548017|gb|T25217.1|T25217
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
EST: gi|211045444|gb|FL056737.1|FL056737
EST:     CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTAT                         GCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC
genomic: CTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGC

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: 1035

TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 683

TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 479

TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 540

TTACTCGCTTGAAGGCTAACAACCCACTTTACGGATCTTCACTGATTGATTATgtgagtaatg ... cttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgaatttttttgcttagatgtttctgtccgtttgaacctgtgcttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTG
                                             cttgtttc  CT-rich tract
     aatttttttgctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaatgttcaatatttcattcaaattaattttatatttcttgaatttttttgcttagatgtttctgtccgtttgaacctgtgcttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT