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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATTGCTCACGGGGTTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagtattttgtgttcattcctcatcatttttttagcgcaacagctatcaattgaacacctatcaattttgttttctcggatctttgaataaactaaccatcttttgtttgcctataattag

Basic information

species Oryza sativa
transcript LOC_Os07g49270.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g49270.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 15
TGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATTGCTCACGGGGTTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagtattttgtgttcattcctcatcatttttttagcgcaacagctatcaattgaacacctatcaattttgttttctcggatctttgaataaactaaccatcttttgtttgcctataattag
 ||||| ||||||||||||||||||||||| ||||| |||||||| ||||| ||  ||||||| |||||||| || ||||| |||||||| || |||||||| | || || |                  |||||||  |   |      ||| |||| |    | |  || | |||   |  ||     | |  || |||  || ||||||  | || |  | ||
CGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaatagt------------------attttttgtgttgattgaacatccattgga----ttttcatatagttgcttgagag----ggactaattaattatattttgtccggctgtgttcag
















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|58694980|gb|CK083667.1|CK083667
EST:     TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAG                         ATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
genomic: TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagta ... ctataattagATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
EST: gi|29671781|gb|CB668056.1|CB668056
EST:     TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAG                         ATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
genomic: TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagta ... ctataattagATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
EST: gi|29671780|gb|CB668055.1|CB668055
EST:     TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAG                         ATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
genomic: TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagta ... ctataattagATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
EST: gi|33675288|gb|CF303527.1|CF303527
EST:     TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAG                         ATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
genomic: TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagta ... ctataattagATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
EST: gi|29663749|gb|CB660024.1|CB660024
EST:     TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAG                         ATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
genomic: TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagta ... ctataattagATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
EST: gi|218478545|gb|FG960299.1|FG960299
EST:     TACTTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTA-CTCA-CTCAG                         ATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTA
genomic: TAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCT-AGCTCAGgtaactagta ... ctataattagATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTA
EST: gi|58593125|gb|CF991433.1|CF991433
EST:     TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAG                         ATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
genomic: TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagta ... ctataattagATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
EST: gi|163926592|gb|EG713608.1|EG713608
EST:     TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAG                         ATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT
genomic: TTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagta ... ctataattagATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTAT

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 1 RNA-Seqlibrary.


Block sizes: 67 (upstream exon), 72 (downstream exon)
Score: 24

TGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATTGCTCACGGGGTTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagta ... ctataattagATTGGTCTTGCCATGTCTCCTTTGAGCAACAACTCATTGTTTATTGATTATCACCGAAACCCTTTCCCAACATTTTTCCTAAGAGGCCTTAACGTTTCTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATTGCTCACGGGGTTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagtattttgtgttcattcctcatcatttttttagcgcaacagctatcaattgaacacctatcaattttgttttctcggatctttgaataaactaaccatcttttgtttgcctataattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA