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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTTCCCTGCATCAAAAACCTATAGGGAATTAGTGTCCTGCTCAAATTGCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttcacttggatgctggtagatcaaattatcttaaaagtcatctgttattgccactgatttgatgttcaaattgcag

Basic information

species Oryza sativa
transcript LOC_Os01g37837.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37837.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G172101_T02 (Zea mays), 5'ss of exon 8
ATGGTTCCCTGCATCAAAAACCTATAGGGAATTAGTGTCCTGCTCAAATTGCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgta------tcttt-tcacttggatgctggtagatcaa--attatcttaaaagtcatctgttattgccactgatttgatgtt-caaattgcag---------------------
|||||||||||||||||| ||||   | || ||||| ||||| ||||| ||||| || |||||  ||||||||||||| || || ||||||||||||||||||      ||| |  ||| | |||  | ||||||     |||    | |    | ||    |  |     | |   || || | |||||| |                     
ATGGTTCCCTGCATCAAAGACCTTCCGAGAGTTAGTATCCTGTTCAAACTGCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAGgtaaaaggttctgtgccacgtagattattgtagatgtgtcattgctctcagcaccttcacccagagtgg--gctaaaatattactaattgctgaatcttaacatttccgaacag
















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|89173717|gb|CI041610.1|CI041610
EST:     TGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: TGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|24468659|gb|CA305608.1|CA305608
EST:     GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|15851150|gb|BI799426.1|BI799426
EST:     GGTATAGTTTATGCCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|89180489|gb|CI044768.1|CI044768
EST:     GCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|88847058|gb|CI001330.1|CI001330
EST:     ACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: ACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|18386014|gb|BM419213.1|BM419213
EST:     GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|29633862|gb|CB638871.1|CB638871
EST:     TTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: TTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|88850119|gb|CI091414.1|CI091414
EST:     GCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|89173694|gb|CI041587.1|CI041587
EST:     GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|58604093|gb|CK014621.1|CK014621
EST:     GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|86415314|gb|CI069717.1|CI069717
EST:     GCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCCATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|27577321|gb|CB000016.1|CB000016
EST:     GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|88903213|gb|CI088751.1|CI088751
EST:     GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|88480715|gb|CI417986.1|CI417986
EST:     GTTATGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
EST: gi|163925426|gb|EG713339.1|EG713339
EST:     GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAG                         AATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT
genomic: GCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACT

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: 64 (upstream exon), 72 (downstream exon)
Score: 20

ATGGTTCCCTGCATCAAAAACCTATAGGGAATTAGTGTCCTGCTCAAATTGCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttc ... caaattgcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACTGCCACTGAGAGGACCCTTTGCTGTATTTTGGAGAACTTCCAGAAGGAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGTTCCCTGCATCAAAAACCTATAGGGAATTAGTGTCCTGCTCAAATTGCACAGATTTTCAAGCAAGGAGACTTGGTATAGGTTATGGCCAGAAAAAGgtatcttttcacttggatgctggtagatcaaattatcttaaaagtcatctgttattgccactgatttgatgttcaaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA