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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTAACCTATGCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaatggtcctatagattattcgccttagatgttattgatttatcgcccctaattttgtcctcacattcttctcatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g09000.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G048012_T01 (Zea mays), 5'ss of exon 5
TTGGTAACCTATGCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaa--aatggtcc-tatagattattcgccttagat--gttattgatttatcgcccctaattttgtcctcacattcttctcatgcag
||||||  ||||| ||||||||||||||||| |||||||||||||||||||||||    ||||| |  |  |||  ||  || ||| || | |  ||   |  ||| ||  ||  | |     ||     ||   | || || ||  | |||
TTGGTATGCTATGTGGACAGGTTAGGAAGAGACACCCCTGGGGTGATGCTAAGGCAGTAAAGgtacacagcaattatctatacagactacttgatttgtttcagttgttttttagttgtattgaa---catctgaatatcctgcttgtacag

upper sequence: LOC_Os01g09000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G032049_T01 (Zea mays), 5'ss of exon 6
TTGGTAACCTATGCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaa--aatggtcctatagattattcgccttagatgttattgatttatcgcccctaattttgtcctcacattcttctcatgcag
||||||  |||||||||||||| |||||||| |||||||||||||||||||||||||  ||||||| ||  |||  |  || | |  | | |  |||  |   ||||  || | |       |||||  |  |  | || ||    |||
TTGGTACACTATGCGGACAGGTCAGGAAGAGACACCCCTGGGGTGATGCTAAGGCGATAAAGgtgcaaagcaattattatacaaaccacttgttttat-ttcaattgtcttttagtt----gttttgaac--atctgctgcttgcacag
















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|7332447|gb|AU085793.1|AU085793
EST:     GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAG                         GATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
genomic: GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaat ... tctcatgcagGATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
EST: gi|89161518|gb|CI099490.1|CI099490
EST:     GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAG                         GATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
genomic: GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaat ... tctcatgcagGATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
EST: gi|58658548|gb|CK047228.1|CK047228
EST:     GCGGACAGGTTAGGAAGATGCACCCCTGGGGTGATGCTAAGGCGAGCAAG                         GATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
genomic: GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaat ... tctcatgcagGATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
EST: gi|88994745|gb|CI036326.1|CI036326
EST:     GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAG                         GATGAAATTGACA-GAAGCTTGCAGAGATATTAGGTCCAA-GACAGATGCT
genomic: GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaat ... tctcatgcagGATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
EST: gi|15846919|gb|BI795195.1|BI795195
EST:     GCGGACAGGTTAGGAAGATGCACCCCTGGGGTGATGCTAAGGCGACCAAG                         GATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAA-GACAGATGCT
genomic: GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaat ... tctcatgcagGATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
EST: gi|86826937|gb|CI268818.1|CI268818
EST:     GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAG                         GATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
genomic: GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaat ... tctcatgcagGATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
EST: gi|58691015|gb|CK079702.1|CK079702
EST:     GCGGACAGGTTAGGAAGATGCACCCCTGGGGTGATGCTAAGGCGACCAAG                         GATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
genomic: GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaat ... tctcatgcagGATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
EST: gi|88903715|gb|CI089253.1|CI089253
EST:     GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAG                         GATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
genomic: GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaat ... tctcatgcagGATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
EST: gi|66928206|gb|CX115054.1|CX115054
EST:     GCGGACAGGTTAGGAAGATGCA-CCCTGGGGTGATGCTAAGGCGACCAAG                         GATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT
genomic: GCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaat ... tctcatgcagGATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCT

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: 35

TTGGTAACCTATGCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaat ... tctcatgcagGATGAAATTGACAAGAAGCTTGCAGAGATATTAGGTCCAAAGACAGATGCTGACAATGTAAAACCAGTGAAAAAGAAAAAGGAAAAAGCAGCAAAAGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTAACCTATGCGGACAGGTTAGGAAGAGGCACCCCTGGGGTGATGCTAAGGCGACCAAGgtgccaaaatggtcctatagattattcgccttagatgttattgatttatcgcccctaattttgtcctcacattcttctcatgcag

- - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - AAGAGG