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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAGACAGAGAATACAGAGAAGCCATAAAATGTTACAGAAATGCTCTGAGGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtgggacatgaatattattttcccctgtcctatctttaagctagtttttatttttaaaacattgacctccacacagacttgtccaacctaatacgt...

Basic information

species Oryza sativa
transcript LOC_Os01g43030.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43030.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G047093_T01 (Zea mays), 5'ss of exon 4
ATCAGACAGAGAATACAGAGAAGCCATAAAATGTTACAGAAATGCTCTGAGGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtgggacatgaatattattttcccctgtcctatctttaagctagtttttatttttaaaac-attgacctccacacagacttgtccaacctaatacgt-
 ||||| ||||||||||||||||| ||||||||||||||||||||  ||||||||||||||||||||||||||||||| |||||| |||| |||||||||||||| |  |  | |  |   ||||      |  ||| ||     | ||       ||   |   | | |||    ||| |  | |    | |   | ||  
GTCAGATAGAGAATACAGAGAAGCTATAAAATGTTACAGAAATGCATTGAGGATTGATCCAGATAACATAGAAATTCTTCGTGACTTGTCCCTTCTCCAGgttggcgtaaattaacaagcgttttttat--ttatattttggcagtggtgagagcattcccattgagtcaccaggtcacgggttcgaagcagcctctccgca
















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|88591151|gb|CI708067.1|CI708067
EST:     GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAG                         GC-CAAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTT
genomic: GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtggga ... tattccacagGCACAAA-TGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTT
EST: gi|88304950|gb|CI671208.1|CI671208
EST:     GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAG                         GCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTA
genomic: GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtggga ... tattccacagGCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTA
EST: gi|88313578|gb|CI671703.1|CI671703
EST:     GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAG                         GCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTA
genomic: GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtggga ... tattccacagGCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTA
EST: gi|88729096|gb|CI752606.1|CI752606
EST:     GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAG                         GCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGC
genomic: GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtggga ... tattccacagGCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGC
EST: gi|88577420|gb|CI674006.1|CI674006
EST:     GGATTGATCCAGATAACATACAAATTCTACGTGACCTGTCACTTCTCCAG                         C
genomic: GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtggga ... tattccacag-
EST: gi|88577420|gb|CI674006.1|CI674006
EST:     GGATTGATCCAGATAACATACAAATTCTACGTGACCTGTCACTTCTCCAG                         C
genomic: GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtggga ... tattccacag-
EST: gi|88587117|gb|CI704845.1|CI704845
EST:     GGATTGATCCAGATAACATACAAATTCTACGTGACCTGTCACTTCTCCAG                         GCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTCA
genomic: GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtggga ... tattccacagGCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTA
EST: gi|58664912|gb|CK053598.1|CK053598
EST:     GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAG                         GCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTA
genomic: GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtggga ... tattccacagGCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTA
EST: gi|88393900|gb|CI684164.1|CI684164
EST:     GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAG                         GCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTA
genomic: GGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtggga ... tattccacagGCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTA

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: 59 (upstream exon), 71 (downstream exon)
Score: 22

ATCAGACAGAGAATACAGAGAAGCCATAAAATGTTACAGAAATGCTCTGAGGATTGATCCAGATAACATAGAAATTCTACGTGACCTGTCACTTCTCCAGgttggtggga ... tattccacagGCACAAATGAGGGACTTGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTAACACTGAAGCCAAATCACCGCATGAACTGGATTGGTTTTGCTGTAGCTC




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