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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactactccttccatctcttctgcggatacctatctgttagtatcttctttgcccactaattaacactaatatcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCAACCCCATCATGTCTGACGCTGAATTCGACCAACTCAAACTCAGATTGAA

Basic information

species Oryza sativa
transcript LOC_Os03g64020.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g64020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G896082_T03 (Zea mays), 3'ss of exon 3
---------------------------gtaagtactactccttccatctcttctgcggatac-----ctatctgtta----gtatcttctttgcccactaattaacactaatatcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCAACCCCATCATGTCTGACGCTGAATTCGACCAACTCAAACTCAGATTGAA
                            ||| | |     ||    ||  |       | |      ||| |    |    ||  | ||  | |  ||||  |  |  |    | ||| ||| |   || || |||   ||  | ||||| ||| |||||||| |  |||||||||| ||||||||||| ||||| |||||| |||| ||||| ||||| ||
gtaagcatttttagttaatttgctccactaactgcctgctctcaagtccttgaaaaaaaaattaatgctaacccccaaggtgtggcgtcgatacaaactacgttcctgtgtgttgtttccagACGAAGATGAGCAAAAGCTTTTGGAAGCTTCCTTGGCCTATACCTCCGGCAACCCAATCATGTCTGATGCTGAGTTCGACGAACTGAAACTTAGATTAAA
















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|218487328|gb|FG968259.1|FG968259
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58694129|gb|CK082816.1|CK082816
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|157651887|gb|EX451521.1|EX451521
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58690623|gb|CK079310.1|CK079310
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58692378|gb|CK081065.1|CK081065
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58591285|gb|CF989593.1|CF989593
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|33801214|gb|CF326480.1|CF326480
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58689767|gb|CK078454.1|CK078454
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58606048|gb|CK034081.1|CK034081
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACA
EST: gi|313081134|gb|HO213720.1|HO213720
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA

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: 73 (upstream exon), 70 (downstream exon)
Score: 112

CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCAACCCCATCATGTCTGACGCTGAATTCGACCAACTCAAACTCAGATTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacctatctgttagtatcttctttgcccactaattaacactaatatcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCAACCCCATCATGTCTGACGCTGAATTCGACCAACTCAAACTCAGATTGAA
                                      cactaat  putative branch site (score: 112)
                                            tatcttttc  CT-rich tract
                               taattaacactaatat  TA-rich tract