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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttgctcctttatttcttcttctatctccttgaattattttcattataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT

Basic information

species Oryza sativa
transcript LOC_Os11g40510.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 1
cttttgctcctttatttcttcttctatctcctt----gaattattttcattataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
 ||||  || ||||   |   | | | || | |     ||| ||     ||||      | |   |  | | ||||  || |||||  |||   |||   ||||||||||||||| || ||||| |||||||||||||| |||||||||||||||||||| || ||
gttttcttcatttaagacaaatgcgaactgcgttatgaaatcatagatgttatctctgttcttcatagaaccttttgctt-acacttgtatgtcttt---gcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 2
cttttgctcctttatttcttcttctatctcc----ttgaattattttcattataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
 ||||  |  ||||  ||   | | | || |    |  ||| ||     ||||      | |   |  | | ||||  || |||||  |||   |||   ||||||||||||||| || ||||| |||||||||||||| |||||||||||||||||||| || ||
tttttctttatttaagtcaaatgcgaactgcgatatgaaatcatagatgttatctctgttcttcatagaaccttttgctt-acacttgtatgtcttt---gcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 1
cttttgctcctttatttcttcttctatctccttgaattattttcattataaaatatttaagtgcaccattttttttgaca-----ctaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
     |   |||||| | |   |  |   |  | | | | | |   |||   || | || |       ||| || |  |       | | ||| || | | |||||||||||| ||  | ||||| || ||||||||||| |||||||||||||||||||| |||||
-----gtgtctttatatatctatgaaatgctctcagtgagtgttgatattttatttctaggatttttttttcttctttctattttttcacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGT

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 1
----cttttgctcctttatttcttcttctatctccttgaattattttcattataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
     | | | |   | ||||       | |||  ||  ||||||||  || |      ||    |      |||| |||     | | ||| || | | |||||||||||| ||    ||||| || ||||||||||| |||||||||||||||||||| |||||
cttgatgtgggtagatgatttaggggcttgtctttttatattatttttgttctttttctttcttttattttcttttcttt----tttacatttttattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGT

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: 67 (upstream exon), 75 (downstream exon)
Score: 73

ATCGATCGATTGAGTGATTGGTTGATTGATCGACATGCAGCATCAGCAGCGGATGAAGCAGGCGGCGGCGGCGGCGCAGCAGCAGCAGATGATGCAGCAGgcgctgctca ... tttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
                                 cactaat  putative branch site (score: 73)
                                         ttattttct  CT-rich tract
                      attttttttgacacta  TA-rich tract