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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttcaaaatcgttgtacccatagtgtcacatgctacattgttttgctagaaatgaggttggactttctccttctcttttgttgctgttttaggta...

Basic information

species Zea mays
transcript GRMZM2G047093_T01
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047093_T01 (Zea mays), 5'ss of exon 25
lower sequence: LOC_Os01g43030.1 (Oryza sativa), 5'ss of exon 25
CATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttcaaaatcgttgtacccatagtgtcacatgctacattgtt--ttgctagaaatgaggttggactttctccttctcttttgttgctgttttaggta
 | ||| ||||||||||||| ||   |||| |||||| ||| |||||||||||||| ||||||||||||||| |||||||||| ||| |||| ||||| |||||||| |||  | |   |||||| | | |  ||   |  |||  |  | ||| | | | |  |   ||||    | |  | |   |  |||  |  |   
AACAGTGTGCTTGGTCCTGTGAATGAATGGAAAATTCTAGACTGTATTGATGTTCACAAATTGCTGGAGACAATCTTTGGTGACCAGGATGTGGCAAACAgtaagttccaatgttgacatacccaaattatttcaccttgtattagtgctcgctggcattaatctgctacttctgtcattgcat--atcactgggtgcgacg
















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|7227463|gb|AW566104.1|AW566104
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|211094638|gb|FL030910.1|FL030910
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|32924622|gb|CF029434.1|CF029434
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
EST: gi|32924627|gb|CF029439.1|CF029439
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
EST: gi|211039204|gb|FL261425.1|FL261425
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|32923660|gb|CF028472.1|CF028472
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTAC
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTAC
EST: gi|32944990|gb|CF049809.1|CF049809
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
EST: gi|60345123|gb|DN212096.1|DN212096
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|211089342|gb|FL470619.1|FL470619
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|211039203|gb|FL261424.1|FL261424
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|32924181|gb|CF028993.1|CF028993
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
EST: gi|32924574|gb|CF029386.1|CF029386
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
EST: gi|32924629|gb|CF029441.1|CF029441
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGT
EST: gi|211406573|gb|FL434917.1|FL434917
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|32923887|gb|CF028699.1|CF028699
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTAC
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTAC
EST: gi|211267719|gb|FL453278.1|FL453278
EST:     GTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: GTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|32923761|gb|CF028573.1|CF028573
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTAC
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTAC
EST: gi|60398052|gb|DN230868.1|DN230868
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|60340635|gb|DN207608.1|DN207608
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|15313502|gb|BI478733.1|BI478733
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|67014809|gb|CO443558.1|CO443558
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|33093540|gb|CF053534.1|CF053534
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTA
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTA
EST: gi|211430406|gb|FL005437.1|FL005437
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|211543406|gb|FL435454.1|FL435454
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|60349287|gb|DN216260.1|DN216260
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|32934431|gb|CF039243.1|CF039243
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTAC
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTAC
EST: gi|211094639|gb|FL030911.1|FL030911
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAG
EST: gi|32923755|gb|CF028567.1|CF028567
EST:     TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATA                         GGTGGAAGGCACGGTGCGCGGAATATTTTCCGTAC
genomic: TGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTAC

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), 46 (downstream exon)
Score: 259

CATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAGGCATCAAGAGCGCTATTTCAACCTATGCCATTGACCATAGTCTCGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

CATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAGGCATCAAGAGCGCTATTTCAACCTATGCCATTGACCATAGTCTCGAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 325

CATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAGGCATCAAGAGCGCTATTTCAACCTATGCCATTGACCATAGTCTCGAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 224

CATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttca ... ttttcaacagGGTGGAAGGCACGGTGCGCGGAATATTTTCCGTACTCGACGTACTTTGAAGGCATCAAGAGCGCTATTTCAACCTATGCCATTGACCATAGTCTCGAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAATAgtaagtttcaaaatcgttgtacccatagtgtcacatgctacattgttttgctagaaatgaggttggactttctccttctcttttgttgctgttttaggta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA