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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGAGCTTGGAGCAATGATGGATCGCATGGAATCTGCGAAACTGAGGACTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttacatcttttacactcatagctgttggcaaattattttgtcaaagagatcaattgtaattttagttcatttttagtgtcagtatgacaataattgaatggatttgcattgtgcaaatattctgctatcttgttcgtgatttcacattatcaatttttcag

Basic information

species Zea mays
transcript GRMZM2G155323_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155323_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g50510.1 (Oryza sativa), 5'ss of exon 7
CAATGAGCTTGGAGCAATGATGGATCGCATGGAATCTGCGAAACTGAGGACTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttacatctttt----acactcatagctgt-tggcaaattattttgtcaaagagatcaattgtaattttagttcatttttagtgtcagtatgacaataattgaatggatttgcattgtgcaaatattctgctatcttgttcgtgatttcacattatcaatttttcag
| |||| |||  ||||||| |||| || ||||||||| | ||| |||| |||||| | |||||||||||||||||||||||||| || || ||||||||||||||||  || | |     |   | ||| |  |    || ||| |||||  ||  | ||| | |  | ||||||   |     | || || ||  ||| | ||| ||                                                               
CGATGAACTTAAAGCAATGGTGGAACGTATGGAATCTTCAAAATTGAGAACTGTTGATCTTACTGACAATGATTTGGCAAAGGATCATCTAAGATACTTTgtaagttggatttctctgccaattttataacaatgccacacatttttttggaaactaaatctaat-cacttttagagta-----aatgacacta--acagtgattaaa---------------------------------------------------------------
















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|74234812|gb|DT642726.1|DT642726
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|26457063|gb|CA828646.1|CA828646
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|32841540|gb|CD981221.1|CD981221
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|32841013|gb|CD980694.1|CD980694
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|32841524|gb|CD981205.1|CD981205
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|50324582|gb|CO519708.1|CO519708
EST:     GTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: GTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|32841290|gb|CD980971.1|CD980971
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|32931996|gb|CF036808.1|CF036808
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|32840967|gb|CD980648.1|CD980648
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|21088934|gb|BQ401247.1|BQ401247
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|45568061|gb|CK985882.1|CK985882
EST:     CTGTTAACCTTACTGACGATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|60344747|gb|DN211720.1|DN211720
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|32840962|gb|CD980643.1|CD980643
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|32841507|gb|CD981188.1|CD981188
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|32841337|gb|CD981018.1|CD981018
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|37383846|gb|CF628958.1|CF628958
EST:     CCTTAGATAC-TT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
EST: gi|60355301|gb|DN222274.1|DN222274
EST:     CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTT                         ATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC
genomic: CTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTC

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: 183

CAATGAGCTTGGAGCAATGATGGATCGCATGGAATCTGCGAAACTGAGGACTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTCCCGGAAAGGCCTGGGGCCCTTATGAAATTTTTGGACACGTTTAGTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

CAATGAGCTTGGAGCAATGATGGATCGCATGGAATCTGCGAAACTGAGGACTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTCCCGGAAAGGCCTGGGGCCCTTATGAAATTTTTGGACACGTTTAGTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 393

CAATGAGCTTGGAGCAATGATGGATCGCATGGAATCTGCGAAACTGAGGACTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTCCCGGAAAGGCCTGGGGCCCTTATGAAATTTTTGGACACGTTTAGTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

CAATGAGCTTGGAGCAATGATGGATCGCATGGAATCTGCGAAACTGAGGACTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttaca ... aatttttcagATTGGAGGAAGATCAGAAATAAAAGATGAACTGGTTTACCGGTTCATTTTCCCGGAAAGGCCTGGGGCCCTTATGAAATTTTTGGACACGTTTAGTCCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATGAGCTTGGAGCAATGATGGATCGCATGGAATCTGCGAAACTGAGGACTGTTAACCTTACTGACAATGATTTGGCAAAGGACCACCTTAGATACTTTgtaagttacatcttttacactcatagctgttggcaaattattttgtcaaagagatcaattgtaattttagttcatttttagtgtcagtatgacaataattgaatggatttgcattgtgcaaatattctgctatcttgttcgtgatttcacattatcaatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG