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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattcatcattatgatcaaaagcaaaggattatgcagtgatgattatcatatctgtctgtatggaaattttcatagaattatctataattgtaac...

Basic information

species Zea mays
transcript GRMZM2G115518_T01
intron # 9
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|110537607|gb|EE041667.1|EE041667
EST:     ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG                         TTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTTTGTGCTGCA
genomic: ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
EST: gi|67016487|gb|CO445236.1|CO445236
EST:     ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG                         TTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
genomic: ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
EST: gi|76013494|gb|DT940664.1|DT940664
EST:     AGTTTCAGCATGCG                         TTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
genomic: AGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
EST: gi|76284391|gb|DV023959.1|DV023959
EST:     ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG                         TTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
genomic: ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
EST: gi|110527857|gb|EE032041.1|EE032041
EST:     ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG                         TTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTTTGTGCTGCA
genomic: ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
EST: gi|211096943|gb|FL476438.1|FL476438
EST:     ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG                         TTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
genomic: ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
EST: gi|31357313|gb|CD441670.1|CD441670
EST:     ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG                         TTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
genomic: ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
EST: gi|211350197|gb|FL470902.1|FL470902
EST:     GAGAATCAAGGGTTCTTGAGTTTCAGCATGCG                         TTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
genomic: GAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
EST: gi|24769079|gb|CA404208.1|CA404208
EST:     ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG                         TTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
genomic: ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
EST: gi|78104805|gb|DV523223.1|DV523223
EST:     ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG                         TTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
genomic: ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
EST: gi|6626368|gb|AW257900.1|AW257900
EST:     ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCG                         TTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
genomic: ACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCA
EST: gi|60357690|gb|DN224663.1|DN224663
EST:     CAAGGGTTCTTGAGTTTCAGCATGCG                         -TGGAAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGC
genomic: CAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGG-AACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGC

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), 44 (downstream exon)
Score: 62

GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCAGCAATCAGCCCGTACCAGCTGGAAGCTTTGGAAAGGTGGGAAGAAATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCAGCAATCAGCCCGTACCAGCTGGAAGCTTTGGAAAGGTGGGAAGAAATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCAGCAATCAGCCCGTACCAGCTGGAAGCTTTGGAAAGGTGGGAAGAAATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattc ... cttatctcagTTGGAACCACTTGCGTACAGAAAGATGGACTTTGAAGAATTCTGTGCTGCAGCAATCAGCCCGTACCAGCTGGAAGCTTTGGAAAGGTGGGAAGAAATTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTGACAAGATACTCAACTGACGCCATGAGAGAATCAAGGGTTCTTGAGTTTCAGCATGCGgtaaggattcatcattatgatcaaaagcaaaggattatgcagtgatgattatcatatctgtctgtatggaaattttcatagaattatctataattgtaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagcaa