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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggtcgctggttatgggcacaattgattgtgttattgttgtgtttatcagcaaaaattgatggaattcgttctgaattaccacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATG

Basic information

species Zea mays
transcript GRMZM2G086489_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086489_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 15
gtaagggtcgctggttatgggcacaattgattgtgttattgttgtgtttatcagcaaaaattgatggaattcgttctgaattaccacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATG
||| |  ||    | || |  ||  |   |   | ||||  |  ||||  ||        ||  ||||  || | |||||| |||| ||| |||||||||||||||||||| ||||||||||  ||| || ||||||| || ||||||||||| |||||||| |||||||| ||||| ||| | |||||||| |
gtatgcatcaaaagata-gttcatgagatac-atattatgatcatgttgctc--------ttactggacctcat-ctgaatgaccaacctgcagGACTACATATATGAAGACGAGTTGCAAAACTTCATTCAGGAGGGTGCACTTTCTGAGCTGATTGTTGCCTTCTCTCGTGAAGGACCAGCCAAAGAATACG
















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|22491259|gb|BU051182.1|BU051182
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|33102735|gb|CF062695.1|CF062695
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|211465903|gb|FL134195.1|FL134195
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTTCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|211465904|gb|FL134196.1|FL134196
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTTCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|32943853|gb|CF048672.1|CF048672
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|15499663|gb|BI596176.1|BI596176
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|32832265|gb|CD971943.1|CD971943
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|67026638|gb|CO455387.1|CO455387
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|31351811|gb|CD436168.1|CD436168
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTTCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|60357924|gb|DN224897.1|DN224897
EST:     TGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: TGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|15632677|gb|BI679770.1|BI679770
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|211465906|gb|FL134198.1|FL134198
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTTCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|32835080|gb|CD974758.1|CD974758
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|67033233|gb|CO461982.1|CO461982
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|19437266|gb|BM953676.1|BM953676
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|32835719|gb|CD975397.1|CD975397
EST:     CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTT

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: 1111

GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 627

GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 864

GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 796

GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaagggtcg ... cacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtgtttatcagcaaaaattgatggaattcgttctgaattaccacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATG
                   aattgat  putative branch site (score: 796)
                                            ccacccttc  putative PPT
                aaaaattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagggtcgctggttatgggcacaattgattgtgttattgttgtgtttatcagcaaaaattgatggaattcgttctgaattaccacccttcagGACTACATATATGAAGATGAGTTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA