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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagtaccttaatgcacagcgaagatatatcaatacatgcctctctcccagttttaggtttccactgaagagcaagtgctcttaggcatataggctttaaagtttgaaggcttacttcaaactttgcatttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACATCCTTTGGAATAACAATGACGGCAAATTTGCTGATCA

Basic information

species Zea mays
transcript GRMZM2G160460_T02
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 15
gtatagtaccttaatgcacagcgaagatatatcaatacatgcctctctcccagttttaggtttccactgaagagcaagtgctcttaggcatataggctttaaagtttgaaggcttacttcaaactttgcatttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACATCCTTTGGAATAACAATGACGGCAAATTTGCTGATCA
||||||   | |    || |          |||| |||   | |       || |  ||     || | |   |    || | || ||   ||  |    |  || ||||| || ||||| ||||| | || |||  |||||||||| ||||| ||||||||||| ||||||||||| ||||| || ||||||||| | ||||||||||||||||||||||| ||||| ||| || | |
gtatagcttcatggctcata----------atca-tacggccttggaatttagctgaagag---cattcacatggccatgatttttggagcatttgtcagatggtctgaagactcacttccaactt-gtatattttcagATCCTCCCGGTTAGTATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCCAACTGGCTTACATCCTTTGGAATAACAATGACAGCAAACTTGATGCTTA

upper sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 15
gtatagtaccttaatgcacagcgaagatatatcaatacatgcctctctcccagttttaggttt-ccactgaagagcaagtgctcttaggcatataggctttaaagtttgaaggctt-acttcaaactttgcatttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACATCCTTTGGAATAACAATGACGGCAAATTTGCTGATCA
||||| | | ||    || |||  | | ||     ||  |   | |    || |   |  |   ||| |     ||||||  ||| ||||||  ||  |    | | | |||  || | || || |||||  | ||  |||||||||||||||||||||||||||||||  |||||||| ||||| |||||||||  | | |||||||  | |||||||||||| ||||||||| |  |||
gtataatgctttgccccatagctcaca-atgatgtta-gtatttttagagcattgacacatccaccattttgttgcaagta-tctcaggcat-cagcttaagtaatctaaagatttcagttaaatctttgtttgttcttagATCCTCCCAGTTAGCATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCA
















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|78105585|gb|DV524003.1|DV524003
EST:     TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAG                         ATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
genomic: TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
EST: gi|32837362|gb|CD977040.1|CD977040
EST:     TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAG                         ATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
genomic: TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
EST: gi|60400681|gb|DN233488.1|DN233488
EST:     TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAG                         ATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
genomic: TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
EST: gi|32839330|gb|CD979011.1|CD979011
EST:     TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAG                         ATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
genomic: TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
EST: gi|60350213|gb|DN217186.1|DN217186
EST:     TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAG                         ATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
genomic: TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
EST: gi|32838171|gb|CD977849.1|CD977849
EST:     TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAG                         ATCCTCCCAGTTAGCATCAAGAGTCTAGACAAAAAGCTTCGCGACCCTTGC
genomic: TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTG-CAGGAAGCTTCGCGACCCTTGC
EST: gi|60344421|gb|DN211394.1|DN211394
EST:     TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAG                         ATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
genomic: TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
EST: gi|78121863|gb|DV540247.1|DV540247
EST:     TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAG                         ATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC
genomic: TTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCC

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: 46 (upstream exon), 43 (downstream exon)
Score: 29

GCTTATGTCATTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACATCCTTTGGAATAACAATGACGGCAAATTTGCTGATCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 139

GCTTATGTCATTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACATCCTTTGGAATAACAATGACGGCAAATTTGCTGATCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 115

GCTTATGTCATTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACATCCTTTGGAATAACAATGACGGCAAATTTGCTGATCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

GCTTATGTCATTGCCTTCTCCTTCGGTATGGGTGCCATTCCTTGGATCATAATGTCTGAGgtatagtacc ... atttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACATCCTTTGGAATAACAATGACGGCAAATTTGCTGATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggcatataggctttaaagtttgaaggcttacttcaaactttgcatttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACATCCTTTGGAATAACAATGACGGCAAATTTGCTGATCA
                          ggcttac  putative branch site (score: 85)
                                            cattttt  putative PPT
             tttaaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagtaccttaatgcacagcgaagatatatcaatacatgcctctctcccagttttaggtttccactgaagagcaagtgctcttaggcatataggctttaaagtttgaaggcttacttcaaactttgcatttttgtagATCCTCCCAGTTAGCATCAAGAGTCTTGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACATCCTTTGGAATAACAATGACGGCAAATTTGCTGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT