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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagtttgaattttgaataacatttgctttgacatgctgatttactctaaactgtacgaagcctgacaaaatggtatctgatcaatttcttgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGGGGCTCTACTACTGCCAGAACATCACCGACCGGGCAATGTACTCGCTGGC

Basic information

species Oryza sativa
transcript LOC_Os01g65920.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65920.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G138176_T01 (Zea mays), 3'ss of exon 4
-----tcagtttgaattttgaataacatttgctttgac--atgctgatttactctaaactgtacgaagcctgacaaa-atggtatctgatcaa----tttcttgatct-------gcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGGGGCTCTACTACTGCCAGAACATCACCGACCGGGCAATGTACTCGCTGGC
     |   ||| |  | ||       |    ||  ||   | | ||  ||| ||  |   |||    ||||||    ||  |  |||  | |     |  | |||||       ||||||||||||||||| || || || || ||||||| ||||||||| || ||||| ||||||||||||||||||||||| ||||| || |||||||| |||||
gtgagttgctttcacgtgtgttgggggtcaaattctactagtacagaactacgctggaacttacctgacctgaccgctattttggctggcccaacgcctgttcgatcttcctgccgcagATGAGAGCGTGGTTGCGCTGGCGAACGGCTGCCTTCACCTGCGCTCCCTGGGTCTCTACTACTGCCAGAACATCACGGACCGCGCCATGTACTCCCTGGC
















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|86539186|gb|CI179392.1|CI179392
EST:     CTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: CTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|4880775|gb|AU065074.1|AU065074
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTNGCTGTGTTCTGATAACAG                         ATGAGAGCGTG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTG
EST: gi|58676252|gb|CK064939.1|CK064939
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|89175635|gb|CI042656.1|CI042656
EST:     GTG-CCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|29673585|gb|CB669860.1|CB669860
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|88206143|gb|CI205992.1|CI205992
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCCTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|218481897|gb|FG957216.1|FG957216
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|86254355|gb|CI059082.1|CI059082
EST:     TGTTCTGATAACAG                         ATGAGAGCGTGTTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: TGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|29646357|gb|CB651364.1|CB651364
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|88993364|gb|CI257792.1|CI257792
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|218505252|gb|FG948340.1|FG948340
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|5003534|gb|AU068683.1|AU068683
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCA-CTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|88356071|gb|CI627519.1|CI627519
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|29643872|gb|CB648879.1|CB648879
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|218478607|gb|FG965535.1|FG965535
EST:     GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG
EST: gi|11564873|gb|AU165509.1|AU165509
EST:     GTGCCCTGAANTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAG                         ATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTNA-CTGCGGTCGCTGG
genomic: GTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGG

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: 57 (upstream exon), 75 (downstream exon)
Score: 50

GGCTGGTGTGATAGTGTAACTGACAAGGGAGTGACCAGCTTGGCATCAGGGTGCCCTGAACTTCGGGCTCTGGACTTGTGTGGCTGTGTTCTGATAACAGgtaatctccg ... tgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGGGGCTCTACTACTGCCAGAACATCACCGACCGGGCAATGTACTCGCTGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaaactgtacgaagcctgacaaaatggtatctgatcaatttcttgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGGGGCTCTACTACTGCCAGAACATCACCGACCGGGCAATGTACTCGCTGGC
                                        tttctt  CT-rich tract
                                   atcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagtttgaattttgaataacatttgctttgacatgctgatttactctaaactgtacgaagcctgacaaaatggtatctgatcaatttcttgatctgcagATGAGAGCGTGGTCGCTCTTGCCAATGGCTGCCCTCACCTGCGGTCGCTGGGGCTCTACTACTGCCAGAACATCACCGACCGGGCAATGTACTCGCTGGC

- - - - - - - - - - catttgc
- - - - - - - - - - - - - - - - catgctg
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgtacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacaaaa