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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttggcactaggaagaatcattattataggaagaatcaagtttttcttattggtgtagttaatcgatttgccttaaactgtgcttctcaaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATTGCAG

Basic information

species Zea mays
transcript GRMZM2G064767_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064767_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g37850.1 (Oryza sativa), 3'ss of exon 3
tgcttggcac-taggaagaatcattattataggaagaatcaagtt-tttcttattggtgtagttaatcgatttgccttaaactgtgcttctcaaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATTGCAG
    |  ||  ||  ||  ||  |  || ||   |   || ||   || | |   | |||  ||     || |   || |    |||||||| |||  ||||||||| |||||||| ||||||||||||||| |  |||| |||||| || ||||||
--tataccatgtattaatgattttctttgtaatgactgtctagcgattgcattgcgctgtgcttctgtcatgttgtttgacacatgcttctctaatgtacagCGGTATCATGCTTATTTCATGGAAGATTTGTCATCACCGATGGTCGTAGTTGCAG
















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|60401609|gb|DN234416.1|DN234416
EST:     CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTG                         CGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
genomic: CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
EST: gi|211367866|gb|FL006735.1|FL006735
EST:     CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTG                         CGGTACCATACTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
genomic: CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
EST: gi|18178433|gb|BM379643.1|BM379643
EST:     CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTG                         CGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
genomic: CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
EST: gi|211370512|gb|FL006740.1|FL006740
EST:     CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTG                         CGGTACCATGCTTACTTCATGGAAGATTTGCCTGTACCAATGGTCATAATT
genomic: CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
EST: gi|37396005|gb|CF635289.1|CF635289
EST:     CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTG                         CGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
genomic: CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
EST: gi|86471640|gb|DY238010.1|DY238010
EST:     AGTTTCCATCATGCTTGGTCTCCCTGGGAGCTG                         CGGTACCATGCTTATTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
genomic: AGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
EST: gi|211367867|gb|FL006736.1|FL006736
EST:     CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTG                         CGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
genomic: CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
EST: gi|71767945|gb|DR965882.1|DR965882
EST:     CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTG                         CGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
genomic: CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
EST: gi|211367870|gb|FL006739.1|FL006739
EST:     CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTG                         CGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
genomic: CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
EST: gi|211367869|gb|FL006738.1|FL006738
EST:     CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTG                         CGGTACCATGCTTACTTCATGGAAGATTTGCCTGTACCAATGGTCATAATT
genomic: CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
EST: gi|91054351|gb|EB164769.1|EB164769
EST:     CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTG                         CGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT
genomic: CCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATT

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), 47 (downstream exon)
Score: 86

CGCGTCTTCGCGGGGTTCCTCCTAGGTTACGTGGCCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATTGCAG


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

CGCGTCTTCGCGGGGTTCCTCCTAGGTTACGTGGCCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 83

CGCGTCTTCGCGGGGTTCCTCCTAGGTTACGTGGCCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

CGCGTCTTCGCGGGGTTCCTCCTAGGTTACGTGGCCTTCCTTGTCTACTCCAGTTTCCATCATGCTTGGTCTCCCTGGGAGCTGgttggtttct ... aaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttattggtgtagttaatcgatttgccttaaactgtgcttctcaaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATTGCAG
             agttaat  putative branch site (score: 100)
                                       cttctca  putative PPT
                                           tcaaattaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttggcactaggaagaatcattattataggaagaatcaagtttttcttattggtgtagttaatcgatttgccttaaactgtgcttctcaaattaacagCGGTACCATGCTTACTTCATGGAAGATTTGCCTGCACCAATGGTCATAATTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA