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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatttcaattatctgtttttgttcaatgtttggagagatattttttgtgtcgacttttgcaaaattttcagctaatcaagtagctatttggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCT

Basic information

species Zea mays
transcript GRMZM2G047867_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047867_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 9
-aaatttcaattatctgtttttgttcaatgtttggagagatattttttgtgtcgacttttgcaaaattt-tcagctaatcaagtagctatttggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCT
    | ||||||   |||   |||| ||||||||||    ||||||| || |    ||  | |  ||     |   ||||| ||| ||||||| |||| ||||||||||||||| |||||||||||||| ||||||||||  |||||||||||| |  |||||| |||||||||||||||| | ||||||||     |||||
tttttatcaatttcatgtagctgtt-aatgtttggacttgtattttt-gtctttttttacgtaccataagctaatgaatcatgtaactatttgcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTTCCTTTCTCCTGTGAATCCAATTGAGAAACTGGAAGGAGCTATGGAAGCT
















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|71333305|gb|DR803709.1|DR803709
EST:     TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAG                         TGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
genomic: TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
EST: gi|5871424|gb|AW017895.1|AW017895
EST:     TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAG                         TGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
genomic: TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
EST: gi|5895598|gb|AW036844.1|AW036844
EST:     TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAG                         TGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
genomic: TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
EST: gi|88757916|gb|DY542057.1|DY542057
EST:     TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAG                         TGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
genomic: TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
EST: gi|5791184|gb|AI977976.1|AI977976
EST:     TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAG                         TGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
genomic: TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
EST: gi|93014144|gb|EB639664.1|EB639664
EST:     CAACATATCCCAG                         TGGGGTCATTGGATTTTTGTTATGTGCAAAAGAAGGTCGGGCAGGGAACTT
genomic: CAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
EST: gi|60350962|gb|DN217935.1|DN217935
EST:     TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAG                         TGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
genomic: TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
EST: gi|88757915|gb|DY542056.1|DY542056
EST:     TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAG                         TGGGGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
genomic: TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
EST: gi|71757236|gb|DR955173.1|DR955173
EST:     TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAG                         TGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
genomic: TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
EST: gi|5847488|gb|AW000567.1|AW000567
EST:     TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAG                         TGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT
genomic: TTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTT

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), 45 (downstream exon)
Score: 38

GGCTGCACACACATCTAATCCAGGATATGCTTGCTATCTGTCGACAGACATTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 52

GGCTGCACACACATCTAATCCAGGATATGCTTGCTATCTGTCGACAGACATTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 158

GGCTGCACACACATCTAATCCAGGATATGCTTGCTATCTGTCGACAGACATTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 161

GGCTGCACACACATCTAATCCAGGATATGCTTGCTATCTGTCGACAGACATTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgca ... ggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtcgacttttgcaaaattttcagctaatcaagtagctatttggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCT
                         agctaat  putative branch site (score: 161)
                                                tttcc  putative PPT
          ttttgcaaaatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatttcaattatctgtttttgttcaatgtttggagagatattttttgtgtcgacttttgcaaaattttcagctaatcaagtagctatttggatttccagTGGTGTCATTGGATTTTTGCTATGTGCAAAAGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - tctgttt
- - - - - - - - - - - - - atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcagct