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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggccccattgtagtttcatttctttacattttttttagcttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcag

Basic information

species Oryza sativa
transcript LOC_Os04g30760.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g30760.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G351023_T01 (Zea mays), 5'ss of exon 5
GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggccccattgtagtttcatttctttacattttttttagcttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcag
||||| |||||||||||||| || |||||||||||||| |||||||||  |  |||||  ||| ||          || |||    |||| | | |    || |    ||||| ||  || ||||  || || || |||| ||
GCTCTAGATAAATGGGGAACGATAGATGTGCTGGTAAATAATGCAGgtatgttcccatgttagatt---------gcactttgcc-agctccttgtttgattgac---tttgtttggcaaataaac-aatattttcttattag

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G099696_T01 (Zea mays), 5'ss of exon 5
GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggccccattgtagtttcatttctt-tacattttttttagcttcctatcatgttaatcaa-tttgtctgtaaattaaaagaacatcttgttatcag
||||| ||||||||||||||||| |||||||||||||| |||||||||  |  | ||   |    |  | | ||  || ||     |  |  | |  ||  ||  |  | ||||| ||| || ||||  || || || |||| ||
GCTCTAGATAAATGGGGAACAATAGATGTGCTGGTAAATAATGCAGgtatgttctcaacttcccatggtatattgcactttgccagttcccacttcccagtttggttgactttgtttgtcaaataaac-aatattttcttattag

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G099696_T02 (Zea mays), 5'ss of exon 4
------------------------------------------------------GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggccccattgtagtttcatttctt-tacattttttttagcttcctatcatgttaatcaa-tttgtctgtaaattaaaagaacatcttgttatcag
                                                      ||||| ||||||||||||||||| |||||||||||||| |||||||||  |  | ||   |    |  | | ||  || ||     |  |  | |  ||  ||  |  | ||||| ||| || ||||  || || || |||| ||
TTTACACCAACCTTTATTACCATGGCTTTATGATTCATGTGTTAATTGAATTAGGCTCTAGATAAATGGGGAACAATAGATGTGCTGGTAAATAATGCAGgtatgttctcaacttcccatggtatattgcactttgccagttcccacttcccagtttggttgactttgtttgtcaaataaac-aatattttcttattag

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G24360.1 (Arabidopsis thaliana), 5'ss of exon 5
GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggccccattgtagtttcatttctttacattttttttagcttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcag
|||||||| ||||||||||| ||||||||  |||| ||||||||||||        |   | ||| |    | |||  ||||  ||||   | ||      |    |   | | |  |                         
GCTCTTGACAAATGGGGAACCATTGATGTTGTGGTTAACAATGCAGgtaaatgaaaaccttggttcc----cattaagttttacttagtaccttactgacgtggcta-catattttcag------------------------

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|14980713|gb|BI305391.1|BI305391
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|23514981|gb|BU673887.1|BU673887
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|30227133|gb|CB965025.1|CB965025
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|30227817|gb|CB965709.1|CB965709
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|23512833|gb|BU672855.1|BU672855
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|30226632|gb|CB964524.1|CB964524
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|30227770|gb|CB965662.1|CB965662
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|87006512|gb|CI294895.1|CI294895
EST:     TGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: TGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|30228838|gb|CB966729.1|CB966729
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|23514324|gb|BU673583.1|BU673583
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
EST: gi|23513544|gb|BU673187.1|BU673187
EST:     GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAG                         GAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG
genomic: GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAG

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: 33 (upstream exon), 75 (downstream exon)
Score: 35

GCTCTTGATAAATGGGGAACAATTGATGTGCTGGTAAACAATGCAGgttgggcccc ... ttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA




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