Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCAGCAAGGCCGCCCGCTTGCCGGCAACATGAAGAAGATCTTCGGCGCCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatcatcaaccaagttccttccttctttcattacatatcaatccttgcagattcaatcaaatcgattcctccctgcag

Basic information

species Zea mays
transcript GRMZM2G092468_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092468_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g01250.1 (Oryza sativa), 5'ss of exon 1
CAACCAGCAAGGCCGCCCGCTTGCCGGCAACATGAAGAAGATCTTCGGCGCCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatc-atcaaccaagttcc--ttccttctttcattacata----tcaatccttgcag-attcaatcaaatcgattcctccctgcag--------
||| |  |    |||||  |    |      |||||||||||||||||||||||||||||| |||| || |||||||  |||||||| || |||||  | ||   | ||  ||   |  ||| |  |||| ||||  |||  ||     ||||| | | ||  |  ||||| |||  ||     |   ||         
CAATCGCCGCCTCCGCCTCCGATTCCTTCCGATGAAGAAGATCTTCGGCGCCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttctgtctttcttgtttcgattccatcttcaattctattctattcaattcatccaccaagcaatcgaatgaatcgaatcaaacaaacccgcag
















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|37622046|gb|CF675099.1|CF675099
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211387542|gb|FL169282.1|FL169282
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211087643|gb|FL395856.1|FL395856
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211439056|gb|FL385005.1|FL385005
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|13562177|gb|BG550397.1|BG550397
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAATTGTATCAAGAAGCTCGACGC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAG-ATCAAGAAGCTCGACGC
EST: gi|5928953|gb|AW056245.1|AW056245
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|87151661|gb|DY396450.1|DY396450
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|32908604|gb|CF013417.1|CF013417
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211211675|gb|FL370026.1|FL370026
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCNCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211449729|gb|FL038161.1|FL038161
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211387544|gb|FL169284.1|FL169284
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|17970239|gb|BM277003.1|BM277003
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|71437048|gb|DR818098.1|DR818098
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|32916309|gb|CF021121.1|CF021121
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211394823|gb|FL369347.1|FL369347
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|32863022|gb|CF002704.1|CF002704
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211439568|gb|FL408949.1|FL408949
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCNCGGCGACACCGTCGATTGAAAAGATCAAGAAGCTCGACGC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGAT-GAAAAGATCAAGAAGCTCGACGC
EST: gi|211161696|gb|FL418714.1|FL418714
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211408542|gb|FL414508.1|FL414508
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211348483|gb|FL394288.1|FL394288
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|76286967|gb|DV026535.1|DV026535
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211434160|gb|FL401089.1|FL401089
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
EST: gi|211387541|gb|FL169281.1|FL169281
EST:     CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGA                         ATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC
genomic: CCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCC

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: 47 (upstream exon), 47 (downstream exon)
Score: 60

CAACCAGCAAGGCCGCCCGCTTGCCGGCAACATGAAGAAGATCTTCGGCGCCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCCGAGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

CAACCAGCAAGGCCGCCCGCTTGCCGGCAACATGAAGAAGATCTTCGGCGCCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCCGAGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 310

CAACCAGCAAGGCCGCCCGCTTGCCGGCAACATGAAGAAGATCTTCGGCGCCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCCGAGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 127

CAACCAGCAAGGCCGCCCGCTTGCCGGCAACATGAAGAAGATCTTCGGCGCCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatca ... ctccctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCCGAGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACCAGCAAGGCCGCCCGCTTGCCGGCAACATGAAGAAGATCTTCGGCGCCAAGAAGAACAAGGATCCGCCGCCCACAATCCAGGACGCAACCGACAGAgtacgtatcatcaaccaagttccttccttctttcattacatatcaatccttgcagattcaatcaaatcgattcctccctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC