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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgcttcgacatcgtctcccttcttattacagcaccatccgtttaggtttgtttctattcaattggctgggggtacctacagtgcttcgagccc...

Basic information

species Zea mays
transcript GRMZM2G058366_T01
intron # 11
splice site 5'
intron type U2

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|148965008|gb|EE015841.2|EE015841
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|211158731|gb|FL327701.1|FL327701
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|211340444|gb|FL354255.1|FL354255
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|211435902|gb|FL357604.1|FL357604
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|20803409|gb|BQ294459.1|BQ294459
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|211522124|gb|FL314742.1|FL314742
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|15100485|gb|BI396276.1|BI396276
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|60353761|gb|DN220734.1|DN220734
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|22472958|gb|BU037438.1|BU037438
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGA
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGA
EST: gi|211093130|gb|FL308874.1|FL308874
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|20301264|gb|BQ164207.1|BQ164207
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCG
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCG
EST: gi|211267809|gb|FL345566.1|FL345566
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|211403760|gb|FL312287.1|FL312287
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|149062811|gb|EE157528.2|EE157528
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|211495186|gb|FL341359.1|FL341359
EST:     ATTTCCTSACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|211477104|gb|FL313896.1|FL313896
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
EST: gi|211165712|gb|FL359024.1|FL359024
EST:     ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAG                         ATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT
genomic: ATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTT

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), 48 (downstream exon)
Score: 170

GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTTTATAGGGGAGCTGACTGCTGTGTTCTTGTATATGATGTCAACGTATCCA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 98

GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTTTATAGGGGAGCTGACTGCTGTGTTCTTGTATATGATGTCAACGTATCCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 71

GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTTTATAGGGGAGCTGACTGCTGTGTTCTTGTATATGATGTCAACGTATCCA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 48

GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgc ... tgaagcttagATATGGGATACGGCAGGACAGGAGCGGTTTCAAAGTCTTGGTGTGGCATTTTATAGGGGAGCTGACTGCTGTGTTCTTGTATATGATGTCAACGTATCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACGTCAACAACAGGTTCAGCAACCAGTACAAGGCCACCATCGGCGCGGATTTCCTCACCAAGGAGGTCCAGATCGACGACCGCCTCTTCACACTGCAGgtctgcttgcttcgacatcgtctcccttcttattacagcaccatccgtttaggtttgtttctattcaattggctgggggtacctacagtgcttcgagccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcccttc