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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctatttattatgaaaaagggtatttacaagtttaacattaagggcttgtttggtcgcatggggaatggaggggattgaggggcatataatccca...

Basic information

species Zea mays
transcript GRMZM2G100707_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100707_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g05660.1 (Oryza sativa), 5'ss of exon 4
GCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtac-tcctatttattatgaaaaagggtattta--caagtttaacattaagggcttgtttggtcgcatggggaatggaggggattgaggggcatataatccca-----------------------------
|||| ||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||| | ||||| |||||||||||||| || |||||||| | | | || || | ||||| | || | ||| | || || | | | || | | | | ||| || | |
GCCCTAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGCCACTGCTACAGGTCTTGTTTGGAACTTCTCATTGAGAATGGTCTGGAAAGgtatattaaaagcaccatttgaatgcatatttggtttgggttgttttgaagttcctgaatgctacatttcacattgcatatgttgtaattccatcaaagctaagtattttattttgcctttcatgtgattag

upper sequence: GRMZM2G100707_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 5'ss of exon 5
GCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctatttattatgaaaaagggtatttacaagttt--aacattaagggcttgtt-tggtcgcatggggaatggaggggattgag---gggcatataatccca--------------------
| || || ||||| ||||||||||| |||||||| |||||||| || || |||||||| || |||||||| ||||| ||||| || | ||| || |||||| | | | || | | ||| ||| |||| | | | || | || || | | ||| | | | ||
GACCCAAGTATGCAGTAAAGTATCATACAGCTGCTGAGAATGCTCTAAGTCACTGCTATAGATCTTGTCTGGAACTTCTCATAGATAGTGGGCTACAAAGgtg-tgtgaagtgaaattctagttttttcttatttttttgcaacaatcaaattctattgtagttttgtgattatctttgtatcctgaactcaagaacttgattttggtctgcatacaacattgcag

upper sequence: GRMZM2G100707_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ30302 (Selaginella moellendorffii), 5'ss of exon 4
GCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctatttattatgaaaaagggtatttacaagtttaacattaagggcttgtttggtcgcatggggaatggaggggattgaggggcatataatccca
| || ||| ||||| ||||||||||||||||| || ||||| ||||| || ||||| ||||||||||| || || || || ||| | | |||||||||||| | || || || | ||| ||| || | |||
GTCCTCGATACGCTGTGAAGTATCACACAGCTGCTGAAAATGCCCTTAGTCATTGCTATAGGTCTTGTCTTGAGCTCCTAATCGAGCACGACCTTGAAAGgtaagtttgtt-atctcaaacctcactgtttgagttttttcttttttgttcttag---------------------------------------------

upper sequence: GRMZM2G100707_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ24833 (Selaginella moellendorffii), 5'ss of exon 4
GCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctatttattatgaaaaagggtatttacaagtttaacattaagggcttgtttggtcgcatggggaatggaggggattgaggggcatataatccca
| || ||| ||||| ||||||||||||||||| || ||||| || || || ||||| ||||||||||| || || || || ||| | | |||||||||||| | || || || | ||| ||| || | |||
GTCCTCGATACGCTGTGAAGTATCACACAGCTGCTGAAAATGCCCTGAGTCATTGCTATAGGTCTTGTCTTGAGCTCCTAATCGAGCACGACCTTGAAAGgtaagtttgtt-atctcaaacctcactgtttgagttttttcttttttgttcttag---------------------------------------------

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|149097071|gb|EE182878.2|EE182878
EST:     CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAG                         CATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
genomic: CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
EST: gi|93015869|gb|EB641389.1|EB641389
EST:     CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAG                         CATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
genomic: CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
EST: gi|71763741|gb|DR961678.1|DR961678
EST:     CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAG                         CATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
genomic: CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
EST: gi|148965131|gb|EE015945.2|EE015945
EST:     CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAG                         CATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
genomic: CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
EST: gi|60342456|gb|DN209429.1|DN209429
EST:     CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAG                         CATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
genomic: CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
EST: gi|149110834|gb|EE294332.2|EE294332
EST:     CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAG                         CATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
genomic: CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
EST: gi|31351359|gb|CD435716.1|CD435716
EST:     CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAG                         CATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
genomic: CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
EST: gi|88754428|gb|DY538569.1|DY538569
EST:     CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAG                         CATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC
genomic: CACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACC

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: 164

GCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACCAGCTGCTCATGTGGCAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

GCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACCAGCTGCTCATGTGGCAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

GCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACCAGCTGCTCATGTGGCAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

GCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctat ... atgtggttagCATTGCTACTGGCTGCATTTACACAGAAGCCAAGAATTATCCTCGTGAACCAGCTGCTCATGTGGCAATAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTCATTGAGAATGGCCTTGAAAGgtactcctatttattatgaaaaagggtatttacaagtttaacattaagggcttgtttggtcgcatggggaatggaggggattgaggggcatataatccca

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