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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATGAGTTGTTTGCAGATGTTTCATTTCTTGTTTTCGTCAGTTCTTGGGTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatgagtaactaatgcatgggtctgtatactttaggggctcggtattaataaaactatgcacttattcttaaatttcag

Basic information

species Zea mays
transcript GRMZM2G315726_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G315726_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g49590.1 (Oryza sativa), 5'ss of exon 4
GCCATGAGTTGTTTGCAGATGTTTCATTTCTTGTTTTCGTCAGTTCTTGGGTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaaga-------tgagta-actaatgcatgggtctgtatactttag---------gggctc---ggtattaataaaact-atgcacttattcttaaatttcag
|| |  ||||| |||| ||||||||||||||| | || ||| ||||||||| | |||| ||||| ||||||||||| |||||||||||||||||||| ||||| | |       | |||    | ||  | ||   | ||||||||||         ||  ||     |||   |||| || ||||  || |||| |||||||||
GCTACCAGTTGCTTGCTGATGTTTCATTTCTTATCTTTGTCTGTTCTTGGGCAGTCCTTCGCCTGATATATTATCCATTCTGGATTCTCTGGAGCACAAGgtagatactacatgttagtgtgttcatatacggagttctatactttagcctttagggggattctataatatcgctaaagcttatgcgtttcttctaaaatttcag
















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|37383937|gb|CF629011.1|CF629011
EST:     TTATATATTATCCGTTCTGGATTCTCTGGAGCACGAG                         CTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGT-GNACGGGC
genomic: TTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTG-ACGGGC
EST: gi|211123441|gb|FL433091.1|FL433091
EST:     GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAG                         CTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC
genomic: GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC
EST: gi|78084141|gb|DV512534.1|DV512534
EST:     GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAG                         CTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC
genomic: GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC
EST: gi|84969762|gb|DV170504.2|DV170504
EST:     GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAG                         CTATGAAGTTGTTTTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC
genomic: GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC

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: 44 (upstream exon), 46 (downstream exon)
Score: 17

GCCATGAGTTGTTTGCAGATGTTTCATTTCTTGTTTTCGTCAGTTCTTGGGTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCCAATATACTACTATGTATTCAACAGTCTTCTCTTCTCTCTACTTGTTCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 485

GCCATGAGTTGTTTGCAGATGTTTCATTTCTTGTTTTCGTCAGTTCTTGGGTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCCAATATACTACTATGTATTCAACAGTCTTCTCTTCTCTCTACTTGTTCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 427

GCCATGAGTTGTTTGCAGATGTTTCATTTCTTGTTTTCGTCAGTTCTTGGGTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCCAATATACTACTATGTATTCAACAGTCTTCTCTTCTCTCTACTTGTTCTA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 13

GCCATGAGTTGTTTGCAGATGTTTCATTTCTTGTTTTCGTCAGTTCTTGGGTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCCAATATACTACTATGTATTCAACAGTCTTCTCTTCTCTCTACTTGTTCTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATGAGTTGTTTGCAGATGTTTCATTTCTTGTTTTCGTCAGTTCTTGGGTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatgagtaactaatgcatgggtctgtatactttaggggctcggtattaataaaactatgcacttattcttaaatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA