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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttgaattttaactcatttcatttaagcttaagttaaacttgttttgtgggcactatctacctggatggcttatttcaatgcattatatatggg...

Basic information

species Zea mays
transcript GRMZM2G553314_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 5'ss of exon 4
GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttgaattttaactcatttcatttaagcttaagttaaacttgttttgtgggcactatctacctggatggcttatttcaatgcattatatatggg-----
|||||||| |||||||| ||||||||||||| |||||||||||||   || ||||||||||||||   ||||||  | || |||||||||||||||| | | ||| ||||||||| |   ||| ||  ||| | | | |||||||| | |||  || | |  |  ||   ||  |   |||  ||||        
GGTTTCTATTATGATGCCTACTACAATGATCTGACATTGAATGAGACACATTTTGGTATCATTGATGCCCAAGCACAGAAAGCTGTTGCGgtatgctcttattttgaactcatttta---aagtttgtgtttacccttttttgtggacgctacttagcagttttactc--tttgacttatttgatattaatctgt
















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|76021644|gb|DT948814.1|DT948814
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTTGAACGCATTGAGGTTCAGCAGGGCAGAAGCTCTT
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTT-GAACGCATTGAGGT-CAGCAGGGCAGAAGCTCTT
EST: gi|149089740|gb|EE179011.2|EE179011
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|22819104|gb|BU499194.1|BU499194
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagG-AAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGA
EST: gi|26457084|gb|CA828667.1|CA828667
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|87153201|gb|DY397990.1|DY397990
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|20507213|gb|BQ279533.1|BQ279533
EST:     TGAGGAGTCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: TGAGGAG-CACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|211033167|gb|FL324568.1|FL324568
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|26559163|gb|CA831398.1|CA831398
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|87157710|gb|DY402499.1|DY402499
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|22542059|gb|BU092497.1|BU092497
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|32933378|gb|CF038190.1|CF038190
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|50334514|gb|CO529640.1|CO529640
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|19058529|gb|BM737196.1|BM737196
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|78092217|gb|DV520591.1|DV520591
EST:     ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: ATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
EST: gi|22490568|gb|BU050491.1|BU050491
EST:     CTAAAAAGGCTGTTGCG                         GAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA
genomic: CTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAA

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: 244

GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAAATGTTTGCTGAGAATGAATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAAATGTTTGCTGAGAATGAATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAAATGTTTGCTGAGAATGAATTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 173

GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttg ... catggtgcagGAAAAGCAACCGTTTGAACGCATTGAGGTCAGCAGGGCAGAAGCTCTTGAAATGTTTGCTGAGAATGAATTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCGgtatgctttgaattttaactcatttcatttaagcttaagttaaacttgttttgtgggcactatctacctggatggcttatttcaatgcattatatatggg

- - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT