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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagactgttatttgaggttagagatgttgttgttgagatcttgtgtcaagtatgttctcatacaatatgtgatgtatttttctcttttttccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG

Basic information

species Zea mays
transcript GRMZM2G090087_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 3
----cagactgttatttgaggttaga-gatgttgttgt-----tgagatcttgtgtcaagtatgttctcatacaatatgtgatgtatttttctcttttttccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG
     |   |  |||||    ||||  ||| ||  |||     ||  ||||  | | |||  | | ||||  |||  ||             | |||||| |  ||  ||||||| || |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
tgactacggttatatttagacttagttgatattactgtgaatctgttatctgctctgaagcgtatcctcaggcaacgtgca----------ttttttttttccggtgcagCCATTTGTAGAGAGTTTATCTAATTGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG
















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|211124834|gb|FL408235.1|FL408235
EST:     CGGTGATAAATTCATCAAAGGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: CGGTGATAAATTCATCAAAG-TTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|211082384|gb|FL402151.1|FL402151
EST:     CGGTGATAAATTCATCAAAGTTGCTTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: CGGTGATAAATTCATCAAAGTTGCT-GAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|67040057|gb|CO466312.1|CO466312
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTGGAGCGAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|148958687|gb|EC904955.2|EC904955
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|211219293|gb|FL379956.1|FL379956
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGG
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGG
EST: gi|94472231|gb|EB701189.1|EB701189
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|211484357|gb|FL369749.1|FL369749
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|211535838|gb|FL377068.1|FL377068
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTYATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|211390609|gb|FL418018.1|FL418018
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|211059652|gb|FL374524.1|FL374524
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|60399068|gb|DN231882.1|DN231882
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|60346857|gb|DN213830.1|DN213830
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|28576035|gb|CB281927.1|CB281927
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|211261878|gb|FL409707.1|FL409707
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCAC
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCAC
EST: gi|149071327|gb|EE159720.2|EE159720
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|211254108|gb|FL390493.1|FL390493
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCC
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCC
EST: gi|211069274|gb|FL419947.1|FL419947
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGG
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGG
EST: gi|60339011|gb|DN205984.1|DN205984
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|211309737|gb|FL424540.1|FL424540
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|211337034|gb|FL418406.1|FL418406
EST:     CGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: CGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGG-AACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
EST: gi|211524408|gb|FL405472.1|FL405472
EST:     ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAG                         CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA
genomic: ACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCA

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: 257

GGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCCTGAACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 118

GGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCCTGAACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 97

GGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCCTGAACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

GGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCCTGAACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAATAAAGgtatgcttag ... ccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagtatgttctcatacaatatgtgatgtatttttctcttttttccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG
                           tgtatttttctctttt  CT-rich tract
                             tatttttctctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagactgttatttgaggttagagatgttgttgttgagatcttgtgtcaagtatgttctcatacaatatgtgatgtatttttctcttttttccttgtatagCCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacaa