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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatctatgggactgaaacagttgatttcctgcag

Basic information

species Zea mays
transcript GRMZM2G165535_T05
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165535_T05 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g58580.1 (Oryza sativa), 5'ss of exon 7
GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtata---aattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatctatgggactgaaacagttgatttcctgcag
||||||||||||||||||||||||||||||| | ||||| || || ||||| ||||| ||||| ||||||||||| ||||| ||||| ||||| ||||||||| |   |||| | ||| || ||  |  |  | || | | |  |  |  ||| ||   ||   |      |   | ||              
GGGTACATTCATAGAGTTCCGAAGTGGAATGCTGAATGTGTCGCCCATAGGGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAGgtacaaacaattctttacaaagagcaataatttgttatcattcaggcaccatgaaacttaactgacttatttactatag--------------

upper sequence: GRMZM2G165535_T05 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA09G39800.1 (Glycine max), 5'ss of exon 8
GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgt-ataaattgtgtactaaaagtcagtaccttt--tcttagtaggagaggatggaataaaatctatgggactgaaacagttgatttcctgcag-------------
||| ||||| || |||||||| ||||| ||| | ||||| || ||||| ||  |||||||||||||||||||| | ||||| |||||||| || || ||||| ||  ||| ||   |  |    | |  ||    | ||        |   || |||   |  | |   |||  | |   | |     ||||              
GGGAACATTTATGGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTGGCCGAAACTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAGgttatgtattttggtttttatcatattctctagaattttcactatccatattgaaatgttaggtgtataactttacc--ctaaaagtttgcaatttaagttctcag

upper sequence: GRMZM2G165535_T05 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA18G46390.1 (Glycine max), 5'ss of exon 8
-GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgt-ataaattgtgtactaaaagtcagtaccttt--tcttagtaggagaggatggaataaaatctatgggactgaaacagttgatttcctgcag------------
 ||| ||||| ||||||||||| ||||| ||| | ||||| || ||||| ||  |||| ||||||||||||||| | ||||| |||||||| || || ||||| ||  ||| ||   |  |   || |  ||    | ||        |   || |||   |    |   | |  |   | | |     ||||             
GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTGGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtattttggtttttatcacattctctagaattttcactatccatattgaaatgttaggcgtataattttat--gctaaaagtttgcaatttaagttctca

upper sequence: GRMZM2G165535_T05 (Zea mays), 5'ss of exon 8
lower sequence: AT2G45790.1 (Arabidopsis thaliana), 5'ss of exon 6
GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatctatgggactgaaacagttgatttcctgcag
||| ||||| || || ||||||| ||||||| | |||||||| || || ||  | ||||| |||||||||||| | |||||||||||||  || ||||||||| ||      ||     |||  || |  ||||||      | || ||  | |   | |  ||  | | || || ||  |||     ||
GGGAACATTTATTGAATTCCGAAATGGAATGCTCAATGTATCACCCATTGGTCGCAACTGCAGCCAAGAAGAAAGAGATGAATTTGAGAGATATGATAAGgtagaagaaac-tatatttagtttgttcaatttctt------atagaatatattttgagcattgtcattcaa-cactt--tttttaaaag

upper sequence: GRMZM2G165535_T05 (Zea mays), 5'ss of exon 8
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 5'ss of exon 7
GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattgtgta--ctaaaagtcagtacctt---ttcttagtaggagaggatggaataaaatctatgggactgaaacagttg-atttcctgcag----------------------------
||| || || ||||||||||||||||| ||| | |||||||| || || ||  ||||||| ||||| ||||| || ||||| ||||| ||||| || |||||||||| |    |  ||   |  ||  |  ||    | | | |  | |    ||| |  ||||  || | | |   | |        ||||| |                             
GGGAACCTTTATAGAGTTCCGAAGTGGGATGCTCAATGTATCACCAATTGGGCGAAACTGCAGCCAGGAAGAGCGTGATGAGTTTGAAAAGTATGACAAGgtataaacttcagatccttcgaagcaaaagattgaactgtcaatttgtgtttgtggcaataaattgattgtatttggataaacatgcatcctgaaacaaacaacacaatttataatcatatcag

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|6020771|gb|AW065579.1|AW065579
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|78118501|gb|DV536885.1|DV536885
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|86471496|gb|DY237866.1|DY237866
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|85151824|gb|DW587525.1|DW587525
EST:     GAAGAAACTGTAGCCCAGAAGAACGTGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|40334667|gb|CK368737.1|CK368737
EST:     GAAGAAACTGTAGCCAAGAAGAACGTGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|76011520|gb|DT938690.1|DT938690
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|71763428|gb|DR961365.1|DR961365
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|45846830|gb|CN070773.1|CN070773
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|14700950|gb|BI233368.1|BI233368
EST:     TTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: TTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|71771666|gb|DR969603.1|DR969603
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|148950412|gb|EC895979.2|EC895979
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|148943663|gb|EC888727.2|EC888727
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|148947648|gb|EC893128.2|EC893128
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|148943662|gb|EC888726.2|EC888726
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|5871104|gb|AW017545.1|AW017545
EST:     GATGAATTTGAGAAGTACGATAAG                         GTGCATACCATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|6056459|gb|AW090849.1|AW090849
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|148947872|gb|EC893365.2|EC893365
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|76280415|gb|DV019983.1|DV019983
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|71299718|gb|DR785869.1|DR785869
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|32909183|gb|CF013995.1|CF013995
EST:     GAAGAAACTGTAGCCAAGAAGAACGTGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|76280414|gb|DV019982.1|DV019982
EST:     GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
EST: gi|32909184|gb|CF013996.1|CF013996
EST:     GAAGAAACTGTAGCCAAGAAGAACGTGATGAATTTGAGAAGTACGATAAG                         GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA
genomic: GAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCA

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: 130

GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 317

GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattg ... tttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAGgtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatctatgggactgaaacagttgatttcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT