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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCCGTGTCGCATGGCACCGCGGCAGCGCCGCTGCCGCCTTTCGCGCGGAGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAGgtgagcacggcggatccctcgcctctcgctgtcttcctcaccgtgatacgctttccttcgcggaattgcgttggttcttgggagccacgatctttggggt...

Basic information

species Zea mays
transcript AC215690.3_FGT002
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC215690.3_FGT002 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g31070.1 (Oryza sativa), 5'ss of exon 1
CCCCCGTGTCGCATGGCACCGCGGCAGCGCCGCTGCCGCCTTTCGC-GCGGAGGAG-GATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAGgtgagca----cggcggatccctcgcctctcgctgtcttcctcaccgtgatacgc-tttccttcgcggaattgcgttggttcttgggagccacgatctttggggt
 |  |||  | ||  ||| ||| |     | || || |  |  ||| | |||||||  ||||   || |   ||||||||||||||| |||||||||||||||||| |     |  |   ||||||  | ||| ||  || |||| ||||    ||| |   ||| |     | | || |||||||| | ||  ||   ||      
-CGGCGTCCCACACCGCATCGCCGTCCTCCTGCGGCGGTGTGGCGCAGAGGAGGAGCAATGGGATGTCGC-CGGTGGTGGCCATGGCCTCCACCATCAACAGgtgaccggatccctctagtccctcctccctccctccctccctccccgtcgcgcgcgtgatcttggtttggtagggtgggttcttgcgcgcttcggggttc-----
















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|74245141|gb|DT653055.1|DT653055
EST:     AGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAG                         GGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCA
genomic: AGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAGgtgagcacgg ... cctttactagGGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCA
EST: gi|32823384|gb|CD963106.1|CD963106
EST:     AGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAG                         GGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCA
genomic: AGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAGgtgagcacgg ... cctttactagGGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCA
EST: gi|74244362|gb|DT652276.1|DT652276
EST:     AGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAG                         GGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCA
genomic: AGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAGgtgagcacgg ... cctttactagGGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCA
EST: gi|18964155|gb|BM660842.1|BM660842
EST:     GGCCATGGCGTCCACCATCAACAG                         GG-CAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCA
genomic: GGCCATGGCGTCCACCATCAACAGgtgagcacgg ... cctttactagGGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCA
EST: gi|6626396|gb|AW257928.1|AW257928
EST:     CACCATCAACAG                         GGTCAAAACTGGCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCA
genomic: CACCATCAACAGgtgagcacgg ... cctttactagGGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCA

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: 208

CCCCCGTGTCGCATGGCACCGCGGCAGCGCCGCTGCCGCCTTTCGCGCGGAGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAGgtgagcacgg ... cctttactagGGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCAAATTACCCATTCACTACCACCTCAAAAGCGGGAGATTTTCGATTCACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

CCCCCGTGTCGCATGGCACCGCGGCAGCGCCGCTGCCGCCTTTCGCGCGGAGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAGgtgagcacgg ... cctttactagGGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCAAATTACCCATTCACTACCACCTCAAAAGCGGGAGATTTTCGATTCACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

CCCCCGTGTCGCATGGCACCGCGGCAGCGCCGCTGCCGCCTTTCGCGCGGAGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAGgtgagcacgg ... cctttactagGGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCAAATTACCCATTCACTACCACCTCAAAAGCGGGAGATTTTCGATTCACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 412

CCCCCGTGTCGCATGGCACCGCGGCAGCGCCGCTGCCGCCTTTCGCGCGGAGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAGgtgagcacgg ... cctttactagGGTCAAAACTGTCAAAGAACCCTATACCCCTCCACGAGAGGTACATCGCCAAATTACCCATTCACTACCACCTCAAAAGCGGGAGATTTTCGATTCACTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCCGTGTCGCATGGCACCGCGGCAGCGCCGCTGCCGCCTTTCGCGCGGAGGAGGATGGCCCGTGGGGTGGTGGTGGCCATGGCGTCCACCATCAACAGgtgagcacggcggatccctcgcctctcgctgtcttcctcaccgtgatacgctttccttcgcggaattgcgttggttcttgggagccacgatctttggggt

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcaccg