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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTGCACAAGCATGGAGCCTACACACACCTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaagacagcaccagatcaattggttgcgcatacttgatatatatggacgagacgtggacactttatagatgagtatatataattaacaactggcgttcgttggctgtctcttttcccctcttgttgcag

Basic information

species Zea mays
transcript GRMZM2G126900_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126900_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g36560.1 (Oryza sativa), 5'ss of exon 9
CCCTGCACAAGCATGGAGCCTACACACACCTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaagacagcaccagatcaattggttgcgcatacttgatatatatggacgagacgtggacactttatagatgagtatatataattaacaactggcgttcgttggctgtctcttttcccctcttgttgcag
||||||||||||||||||||||||  || |||||| ||||||||||||||||||||||||| ||||||| |||||||||||||| ||        ||||||  ||       |||| ||| || ||||| |     |  || ||    |  | |||| |   | |  |   ||                                         
CCCTGCACAAGCATGGAGCCTACATGCATCTGATGAACGATGAGGACAAGGAGAACCTCAAATGGCTGCGTGTGTTCAAgtaagcca--------ccagattgatcaccc-tgcat-cttaatgtatatagtatgaaaatgtac----tgaacatgaatggttttcttctgcag----------------------------------------
















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|88752034|gb|DY536175.1|DY536175
EST:     CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAA                         CAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
genomic: CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
EST: gi|31363556|gb|CD447913.1|CD447913
EST:     CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAA                         CAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
genomic: CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
EST: gi|78119916|gb|DV538300.1|DV538300
EST:     CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAA                         CAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
genomic: CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
EST: gi|60396286|gb|DN229155.1|DN229155
EST:     CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAA                         CAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
genomic: CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
EST: gi|14996932|gb|BI319072.1|BI319072
EST:     CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAA                         CAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
genomic: CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
EST: gi|15554177|gb|BI644175.1|BI644175
EST:     CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAA                         CAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
genomic: CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
EST: gi|15057218|gb|BI361190.1|BI361190
EST:     CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAA                         CAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
genomic: CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
EST: gi|45847402|gb|CN071345.1|CN071345
EST:     CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAA                         CAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
genomic: CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
EST: gi|14996904|gb|BI319057.1|BI319057
EST:     CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAA                         CAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
genomic: CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
EST: gi|76923453|gb|DV169495.1|DV169495
EST:     TGATGGACGATGAGGACAAGGAGAACCTNCA-GTGGCTGCATGTGTTCAA                         CAAGTATGACCTGTACGGCCAGAGCAACAGCAGGATCGACGTGGAGGAGGT
genomic: TGATGGACGATGAGGACAAGGAGAACCT-CAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
EST: gi|211354362|gb|FL217076.1|FL217076
EST:     CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAA                         CAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT
genomic: CTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGT

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: 31 (upstream exon), 34 (downstream exon)
Score: 3

CCCTGCACAAGCATGGAGCCTACACACACCTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGTGAAGCCCTACTACATGTCCCTAATCGACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 636

CCCTGCACAAGCATGGAGCCTACACACACCTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGTGAAGCCCTACTACATGTCCCTAATCGACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 359

CCCTGCACAAGCATGGAGCCTACACACACCTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGTGAAGCCCTACTACATGTCCCTAATCGACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

CCCTGCACAAGCATGGAGCCTACACACACCTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaag ... cttgttgcagCAAGTATGACCTGTACAGCAAGAGCAACAGCAGGATCGACGTGGAGGAGGTGAAGCCCTACTACATGTCCCTAATCGACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTGCACAAGCATGGAGCCTACACACACCTGATGGACGATGAGGACAAGGAGAACCTCAAGTGGCTGCATGTGTTCAAgtaagacaagacagcaccagatcaattggttgcgcatacttgatatatatggacgagacgtggacactttatagatgagtatatataattaacaactggcgttcgttggctgtctcttttcccctcttgttgcag

- - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA