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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATCCGCCGTGCGCACGCCGTGCATCCCATCACCGCCGTGCAGATGGAGTGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctgctctccatcaccaattaggcttattccaccaagttcattagagttcaattgtggttctgatcgattaacacgaattcctttgtactctatggtctacag

Basic information

species Zea mays
transcript GRMZM2G176903_T01
intron # 3
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|148939129|gb|EC883560.2|EC883560
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|71305516|gb|DR788901.1|DR788901
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTTGGCCGTGGAATTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATT-GGCCGTGGATTTT
EST: gi|71769569|gb|DR967506.1|DR967506
EST:     CCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: CCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|60394069|gb|DN226939.1|DN226939
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCACGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|91052484|gb|EB162902.1|EB162902
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|67012842|gb|CO441591.1|CO441591
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|93011745|gb|EB637265.1|EB637265
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|149075226|gb|EE163727.2|EE163727
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|91873626|gb|EB403583.1|EB403583
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATT
EST: gi|76291653|gb|DV031221.1|DV031221
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|71441912|gb|DR822962.1|DR822962
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAA                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGG
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGG
EST: gi|148968047|gb|EE019380.2|EE019380
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|71449217|gb|DR830267.1|DR830267
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|149084348|gb|EE173792.2|EE173792
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGAATGGGAATTGTGGCTTACAGTC-AATTGGCCGTGGATTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGG-AATTGTGGCTTACAGTCCAATTGGCCGTGGATTT
EST: gi|44901166|gb|CK827711.1|CK827711
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCACGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|71763494|gb|DR961431.1|DR961431
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|71313076|gb|DR793065.1|DR793065
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|71769570|gb|DR967507.1|DR967507
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|71313078|gb|DR793066.1|DR793066
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|76932705|gb|DV173124.1|DV173124
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATT
EST: gi|91877438|gb|EB407395.1|EB407395
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|32834502|gb|CD974180.1|CD974180
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCACGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|93016813|gb|EB642333.1|EB642333
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
EST: gi|50324103|gb|CO519229.1|CO519229
EST:     TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAG                         AGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT
genomic: TGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTT

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: 148

CAATCCGCCGTGCGCACGCCGTGCATCCCATCACCGCCGTGCAGATGGAGTGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 77

CAATCCGCCGTGCGCACGCCGTGCATCCCATCACCGCCGTGCAGATGGAGTGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 68

CAATCCGCCGTGCGCACGCCGTGCATCCCATCACCGCCGTGCAGATGGAGTGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 78

CAATCCGCCGTGCGCACGCCGTGCATCCCATCACCGCCGTGCAGATGGAGTGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctg ... tggtctacagAGAATTGGGGATTGGAATTGTGGCTTACAGTCCAATTGGCCGTGGATTTTTTGGTGGAAGAGGAGTGATACAGCAAGTTTCTTCTGAATCTAGTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATCCGCCGTGCGCACGCCGTGCATCCCATCACCGCCGTGCAGATGGAGTGGTCGCTCTGGTCCCGAGACATCGAGCCCGAGATCGTGCCACTCTGCAGgtgagctctgctctccatcaccaattaggcttattccaccaagttcattagagttcaattgtggttctgatcgattaacacgaattcctttgtactctatggtctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG