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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttctaggctctcattgatcaggttgcttaatgctcactagtgttacgttaggatttttttttcgctaactcattttggtgattttatgccagattatagaatcaataccttttttttttaatgtatgtatcaacaaatctgaaaagtcacttacagtaaccttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG

Basic information

species Oryza sativa
transcript LOC_Os07g26610.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G069676_T03 (Zea mays), 3'ss of exon 2
gtgtgttctaggctctcattgatcaggttgcttaatgctcactagtgttacgttaggatttttttttcgctaactcattttggtgattttatgccagattatagaatcaataccttttttttttaatgtatgtatcaacaaatctgaaaagtcacttacagtaaccttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG
                                                                     | |  |||  |    | ||   |||   ||| |||  | | ||  |||  |     ||| ||| ||   ||| | ||| |  |  ||||||||||| ||||||||||||||||||||| |||  |||||    || |||| ||||||||| ||| | ||||| || ||||||||
---------------------------------------------------------------------caatgtcagatcacagcttgggtgctt-attttaggtttagtatatttaat-----atgcatgcatgtccaagtgtgagatattgcttacagtaac-ttcattgcagCTGCTCAAGGTGGCACTGTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAG
















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|58603545|gb|CK014073.1|CK014073
EST:     ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATGgtgtgttcta ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|58661803|gb|CK050483.1|CK050483
EST:     ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATGgtgtgttcta ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88355792|gb|CI626233.1|CI626233
EST:     ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATGgtgtgttcta ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88372673|gb|CI612601.1|CI612601
EST:     ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATGgtgtgttcta ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88387369|gb|CI580714.1|CI580714
EST:     ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATG                         CTGCTCAAGGTAGTAGCGTTGTCCCATCCTCTGCGAAAGTT
genomic: ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATGgtgtgttcta ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTT
EST: gi|88732757|gb|CI755934.1|CI755934
EST:     ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATGgtgtgttcta ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|33678513|gb|CF306752.1|CF306752
EST:     ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATGgtgtgttcta ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|33381367|gb|CF196710.1|CF196710
EST:     TCCAGCAAACAAGCATATATTAGCTGCAATG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: TCCAGCAAACAAGCATATATTAGCTGCAATGgtgtgttcta ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88739121|gb|CI762629.1|CI762629
EST:     ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATGgtgtgttcta ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88300211|gb|CI582445.1|CI582445
EST:     ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: ATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATGgtgtgttcta ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA

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: 50 (upstream exon), 58 (downstream exon)
Score: 12

GAATGTAGACTAAGACTGGCTGGTACTTCAGCCAAGTGGTTAAATACAATATCAACAGCATGGATTAGCTCCAGCAAACAAGCATATATTAGCTGCAATGgtgtgttcta ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatgtatgtatcaacaaatctgaaaagtcacttacagtaaccttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG
                                     cagtaac  putative branch site (score: 12)
                                           ccttcatt  CT-rich tract
       tatgtat  TA-rich tract