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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttctcttattaggtcattgtcataaacctgagttagtgggtaggattttgacttctgagtttctcctttag

Basic information

species Zea mays
transcript GRMZM5G824600_T02
intron # 5
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|148969452|gb|EE020260.2|EE020260
EST:     AATCTGGCTCAGTTGTTGCTGTTT--GGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|211527705|gb|FL414610.1|FL414610
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|149055770|gb|EE156478.2|EE156478
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|60343794|gb|DN210767.1|DN210767
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|148972824|gb|EE023810.2|EE023810
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTGGGACTTGCA                         GGTGCTGAGGGAGCAAA-GCCTGCTGGGGCTTCTCGAGTTATTGGCA
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGC-TGCTGGTGCTTCTCGAGTTATTGGCA
EST: gi|74034792|gb|DT535283.1|DT535283
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|78077865|gb|DV506290.1|DV506290
EST:     CAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: CAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|149107259|gb|EE189142.2|EE189142
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|149001497|gb|EE038802.2|EE038802
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|211392726|gb|FL395705.1|FL395705
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GNTGCTGAGGGAGCAAAAGCTGCTGG
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGG
EST: gi|148930859|gb|EC873272.2|EC873272
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|84980410|gb|DW530759.1|DW530759
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTC
EST: gi|211288478|gb|FL412711.1|FL412711
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|211271449|gb|FL402756.1|FL402756
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|211087315|gb|FL378413.1|FL378413
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|148971977|gb|EE022778.2|EE022778
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGCGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|31355494|gb|CD439851.1|CD439851
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|78092172|gb|DV520546.1|DV520546
EST:     TTTTTGGCCTTGGAACAGTGGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: TTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|31355047|gb|CD439404.1|CD439404
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|31355865|gb|CD440222.1|CD440222
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|211356389|gb|FL426375.1|FL426375
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|166505655|gb|EG169502.1|EG169502
EST:     GGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGC
genomic: GGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGC
EST: gi|211284800|gb|FL428470.1|FL428470
EST:     TTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: TTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|149103654|gb|EE289058.2|EE289058
EST:     AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|60344516|gb|DN211489.1|DN211489
EST:     CTTGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: CTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
EST: gi|110515671|gb|EE020259.1|EE020259
EST:     AATCTGGCTCAGTTGTTGCTG--TTGGGCCTGGGAACAGTTGGACTTGCA                         GTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC
genomic: AATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGAC

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: 654

GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 775

GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 472

GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 447

GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttct ... tctcctttagGTTGCTGAGGGAGCAAAAGCTGCTGGTGCTTCTCGAGTTATTGGCATTGACATCGACAATAAAAAGTTTGATGTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTGGAGCGGTGTGGAATACTGCAAAGGTTGAATCTGGCTCAGTTGTTGCTGTTTTTGGCCTTGGAACAGTTGGACTTGCAgtaagtttctcttattaggtcattgtcataaacctgagttagtgggtaggattttgacttctgagtttctcctttag

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT