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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtccccattaggatttggtttgatgtgcattctccatgtatttgttgcttaattcttgcttgtactttaaatcactcagGTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGATTCAAACATTGAGAAGATTTTGGCATTGCTCTTTAATCACTGTGAAAGTG

Basic information

species Oryza sativa
transcript LOC_Os02g07120.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G168629_T04 (Zea mays), 3'ss of exon 22
gtttgtccccattaggatttgg--tttgatgtgcattctccatgtatttgttgcttaattcttgcttgtactttaaatcactcagGTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGATTCAAACATTGAGAAGATTTTGGCATTGCTCTTTAATCACTGTGAAAGTG
|||| |  | ||| | |||| |   || |  ||||||| |||| ||  |||||| |||  | |||| |||||  ||| |   |||||||| |  || || |||||||| |||||||||||||||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||
gtttatttctatttgaattttgatcttaaaatgcattccccatctaactgttgcctaacacatgctcgtactaaaaaactgccagGTAATCGTGCGACAATCTGTTGATCATACTGGCCAGAGTGAGCTACAGGATTCAAACATTGAGAAGATATTGGCATTGCTCTTCAATCACTGTGAAAGTG
















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|88574134|gb|CI665903.1|CI665903
EST:     TTGACAACCAACAGAAGAAACAGTATCTATTGCTTCATTCACTGAAAGAG                         GTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGAT
genomic: TTGACAACCAACAGAAGAAACAGTATCTATTGCTTCATTCACTGAAAGAGgtttgtcccc ... aatcactcagGTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGAT
EST: gi|58610939|gb|CK038651.1|CK038651
EST:     TTGACAACCAACAGAAGAAACAGTATCTATTGCTTCATTCACTGAAAGAG                         GTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGAT
genomic: TTGACAACCAACAGAAGAAACAGTATCTATTGCTTCATTCACTGAAAGAGgtttgtcccc ... aatcactcagGTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGAT
EST: gi|33796960|gb|CF324343.1|CF324343
EST:     TTGACAACCAACAGAAGAAACAGTATCTATTGCTTCATTCACTGAAAGAG                         GTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGAT
genomic: TTGACAACCAACAGAAGAAACAGTATCTATTGCTTCATTCACTGAAAGAGgtttgtcccc ... aatcactcagGTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGAT
EST: gi|29625622|gb|CB630633.1|CB630633
EST:     TTGACAACCAACAGAAGAAACAGTATCTATTGCTTCATTCACTGAAAGAG                         GTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGAT
genomic: TTGACAACCAACAGAAGAAACAGTATCTATTGCTTCATTCACTGAAAGAGgtttgtcccc ... aatcactcagGTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGAT

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: 47 (upstream exon), 72 (downstream exon)
Score: 17

CATTGCTGTTGGAAATTTATCGAAGTATTTGCCTTTTATCTTGAATCAGATTGACAACCAACAGAAGAAACAGTATCTATTGCTTCATTCACTGAAAGAGgtttgtcccc ... aatcactcagGTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGATTCAAACATTGAGAAGATTTTGGCATTGCTCTTTAATCACTGTGAAAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcattctccatgtatttgttgcttaattcttgcttgtactttaaatcactcagGTAATTGCACGGCAGTCTGTTGACCATACTGGCCAGAGTGAGCTCCAGGATTCAAACATTGAGAAGATTTTGGCATTGCTCTTTAATCACTGTGAAAGTG
                      gcttaat  putative branch site (score: 17)
                                      tactttaaat  TA-rich tract