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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctcttttattgcatacaagattggatccaaccatacactagttttctgattggtcgattgtggcagacatcttgcctaaagttctgctctatacc...

Basic information

species Zea mays
transcript GRMZM5G818887_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G818887_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 5
GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctcttttattgcatacaagattggatccaaccatacactagttttctgattggtcgattgtggcagacatcttgcctaaagttctgctctatacc---
||| | ||| |||| ||||| ||| |||||||||| || |||||||||||||| |||| ||| || |||||||| |||||||| |||||||||||||||||  ||           |  |  | |    |||||   |  |   |   |||    |   || |    | |  |||     |||      
GCTACCGCTCAACCTTCATATTTTGTCGCAGAAGAGCCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCACgtaagctcttttatttgatcttcatgctttttaagtcttttgttagttggttagt--attagttgccttat-tatgtgttattagtttccatattatcttcct

upper sequence: GRMZM5G818887_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 5'ss of exon 5
GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctcttttattgcatacaagattggatccaaccatacactagtt--ttctgattggtcgattgtggcagac-atcttgcctaaagttctgctctatacc
                               |||| || |||||||||||||| |||| ||| || |||||||| |||||||| |||||||||||||||||  ||           |  |  | |    | |||  |  |  | |    ||| ||    |  |  ||   ||   |  | |||      
-------------------------------AAGAGCCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCACgtaagctcttttatttgatctgcatgctttttaagtctttagttggttagtattagtcgccttattatgttttattagtttttatactatcttcctcctc---
















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|211435031|gb|FL327502.1|FL327502
EST:     CAGAAGATGACAACATTCTTCCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CAGAAGATGACAACATTCTT-CATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|148960724|gb|EE011368.2|EE011368
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|32809166|gb|CD961400.1|CD961400
EST:     CCAGAAGATGACAACGTTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|78113030|gb|DV531424.1|DV531424
EST:     TCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: TCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|32804145|gb|CD956381.1|CD956381
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAA-CTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|71313247|gb|DR793147.1|DR793147
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|148971663|gb|EE022386.2|EE022386
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|50331764|gb|CO526890.1|CO526890
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|78091451|gb|DV519825.1|DV519825
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|149045355|gb|EE047779.2|EE047779
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|76013821|gb|DT940991.1|DT940991
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|60342765|gb|DN209738.1|DN209738
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|76013820|gb|DT940990.1|DT940990
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|71313249|gb|DR793148.1|DR793148
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|60341702|gb|DN208675.1|DN208675
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|78091450|gb|DV519824.1|DV519824
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|78022213|gb|DV490600.1|DV490600
EST:     CAGAAGATGACAACATTCTTCATACCAGAACATATGATG-TAGGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACG
genomic: CAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTA-GCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACG
EST: gi|211389689|gb|FL031640.1|FL031640
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|32826943|gb|CD966621.1|CD966621
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|110482572|gb|EE011367.1|EE011367
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|60393918|gb|DN226788.1|DN226788
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|37374451|gb|CF623583.1|CF623583
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|87156323|gb|DY401112.1|DY401112
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|78113031|gb|DV531425.1|DV531425
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|76016276|gb|DT943446.1|DT943446
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
EST: gi|76016277|gb|DT943447.1|DT943447
EST:     CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC                         GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA
genomic: CCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGA

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: 81

GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctctt ... cctattgcagGTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAACgtaagctcttttattgcatacaagattggatccaaccatacactagttttctgattggtcgattgtggcagacatcttgcctaaagttctgctctatacc

- - - - - - - - - - - - - - - - - - - - AAGATG