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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaatcaatccccaaatattttatcttgatattgtagatttgtagcattataaaaaactcgtccctccgtgcattatattaagaagaagatctt...

Basic information

species Zea mays
transcript GRMZM5G844173_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844173_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g08700.1 (Oryza sativa), 5'ss of exon 8
GTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaatcaatccccaaatattttatcttga-tattgtagatttgtagcattataaaaaactcgtccctccgtgcattatattaagaagaagatctt
|||| | || || ||||||||||| || ||||||||||| |||||||||||||| |||||||||||||||||       ||| || |||| ||| | || || | || | | |  || ||  ||||     ||  |  ||| | || |||  |  || | 
GTGTGGTGGAGTCATGGGAAAATACGCAGCTGGTGGAGAATTGAAGCCTCCAACAACTGgttggtaaaatcagcaatggaattttctatcgtgaattttttataattattgtaacattaattactcccatgtctttttattctgttgagat-accatgtg

upper sequence: GRMZM5G844173_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 5'ss of exon 6
GTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaatcaatccccaaatattttatcttgatattgtagatttgtagca-ttataaaaaactcgtccctccgtgcattatattaagaagaagatctt---------------------------------------------------------------------
|||||| ||||||||||| ||||||||||||   |||||| | ||||| ||||| | ||||  ||  ||  ||| ||    || | |  | ||  | || |  ||  |   | || | |  ||        | |   || |   || | ||     | |                                                                      
GTGTAGTGGTGTAATGGGTAAATATGCTGCT---GGAGAGCTCAAGCCGCCAACCATTGgtgagttcaag-aattccatgttaatatcccctggaactggattttgatgataattctgatcaatagagttgttctatcacttcgttcataaatgtgtatccatcacctgtggctatagaatgtgttttgagttgcttcctataactttcatgttgtcctactttggcag
















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|32842002|gb|CD981683.1|CD981683
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCTA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|32842384|gb|CD982065.1|CD982065
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCTA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|148956314|gb|EC902116.2|EC902116
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAG
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAG
EST: gi|32842680|gb|CD982361.1|CD982361
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCTA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|32842398|gb|CD982079.1|CD982079
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCTA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|32842301|gb|CD981982.1|CD981982
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCTA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|32842595|gb|CD982276.1|CD982276
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCTA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|32842361|gb|CD982042.1|CD982042
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCTA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|32842489|gb|CD982170.1|CD982170
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCTA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|32922209|gb|CF027021.1|CF027021
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGTCGAGGATCTGGAAAGCACCCACAACTTATGCCTTGCACCCCCA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|32923012|gb|CF027824.1|CF027824
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|32842370|gb|CD982051.1|CD982051
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCTA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|32841992|gb|CD981673.1|CD981673
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCTA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA
EST: gi|32841997|gb|CD981678.1|CD981678
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCTA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCA

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), 49 (downstream exon)
Score: 257

GTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 271

GTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 186

GTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 241

GTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaa ... ggtgatttagCTTACAGCCGAGGATCTGGAAAGCACCCACAACTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgttggtaaaatcaatccccaaatattttatcttgatattgtagatttgtagcattataaaaaactcgtccctccgtgcattatattaagaagaagatctt

- - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - TGCTGC
- - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccctccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaagaa