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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTTTGCAAGATATTTCGCCCCTTCCCCAGGAAGCACATCTCGCCCCTCCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttacaaagaacttagttaatttctgtgtgcaatggctcttggatctagaactaatatataatttagctataattgtggtggcttttcgaagatt...

Basic information

species Zea mays
transcript GRMZM2G157316_T01
intron # 7
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|5804682|gb|AI979652.1|AI979652
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|18172562|gb|BM347950.1|BM347950
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|86470246|gb|DY236616.1|DY236616
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|18170113|gb|BM339953.1|BM339953
EST:     ACAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|18174318|gb|BM349706.1|BM349706
EST:     CCAGAAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|74237514|gb|DT645428.1|DT645428
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|76281473|gb|DV021041.1|DV021041
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|71759350|gb|DR957287.1|DR957287
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|88748362|gb|DY532503.1|DY532503
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|71327755|gb|DR800511.1|DR800511
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|74232243|gb|DT640157.1|DT640157
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|86470086|gb|DY236456.1|DY236456
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|78076077|gb|DV504511.1|DV504511
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|18162122|gb|BM331961.1|BM331961
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|28985536|gb|CB350690.1|CB350690
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|111192662|gb|EE290798.1|EE290798
EST:     CATAGAGGCCGTGGGGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCCTC
genomic: CATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGT-CCTC
EST: gi|71450334|gb|DR831384.1|DR831384
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|28986640|gb|CB351236.1|CB351236
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|6020337|gb|AW065265.1|AW065265
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|12968576|gb|BG265522.1|BG265522
EST:     CCAGGAGTCTTGTTGGGAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|78022528|gb|DV490915.1|DV490915
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|93013208|gb|EB638728.1|EB638728
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|33091544|gb|CF051538.1|CF051538
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|110532788|gb|EE036968.1|EE036968
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|45568649|gb|CK986167.1|CK986167
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|18165927|gb|BM335766.1|BM335766
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGACCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|76282774|gb|DV022342.1|DV022342
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|71433037|gb|DR814087.1|DR814087
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|71417979|gb|DR804274.1|DR804274
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|86470930|gb|DY237300.1|DY237300
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|111189834|gb|EE287970.1|EE287970
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|71305917|gb|DR789089.1|DR789089
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|76914064|gb|DV165396.1|DV165396
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
EST: gi|76017526|gb|DT944696.1|DT944696
EST:     CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAG                         AATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC
genomic: CCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCC

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: 37

ATTTTTTGCAAGATATTTCGCCCCTTCCCCAGGAAGCACATCTCGCCCCTCCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCCGTTGCTATGCTGGTCTCAATGGGCTTTGATGGCAATAACGCAAGGCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 31

ATTTTTTGCAAGATATTTCGCCCCTTCCCCAGGAAGCACATCTCGCCCCTCCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCCGTTGCTATGCTGGTCTCAATGGGCTTTGATGGCAATAACGCAAGGCAGG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 35

ATTTTTTGCAAGATATTTCGCCCCTTCCCCAGGAAGCACATCTCGCCCCTCCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCCGTTGCTATGCTGGTCTCAATGGGCTTTGATGGCAATAACGCAAGGCAGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 82

ATTTTTTGCAAGATATTTCGCCCCTTCCCCAGGAAGCACATCTCGCCCCTCCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttac ... tctcaagcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCCGTTGCTATGCTGGTCTCAATGGGCTTTGATGGCAATAACGCAAGGCAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTTTTGCAAGATATTTCGCCCCTTCCCCAGGAAGCACATCTCGCCCCTCCAGGAGTCTTGTTGGAAACACACCGTCCCATAGAGGCCGTGCTGTTCAGgttaccttacaaagaacttagttaatttctgtgtgcaatggctcttggatctagaactaatatataatttagctataattgtggtggcttttcgaagatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaagaa