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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtagattagccttgtcgtttattctattgttttcttatttaattactaatttactatgtttctctactcacaacgtcttactcacatgcctttttctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT

Basic information

species Oryza sativa
transcript LOC_Os11g13694.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g13694.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G011575_T02 (Zea mays), 3'ss of exon 9
------------------------------------------gtatgtagattagccttgtcgttt---------attctattgttttcttatttaattact-----aatttactatgtttctctactcacaacgtcttactcacatgcctttttctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT
                                          |||  ||   |    || ||  ||           ||    | ||||   |   | || |     || ||| | || || | |   ||   | | || | ||| |||||| || || ||||| |||||||||  | |||| || ||||| |||||| | |||||||||||||| |||||  |||||||||| ||||||| | |||||||||||||  |||||
gtatgcatacttagccttttcatttgttttatctttatccttgtaattattgtgcttttttctctttgagacaaaggtcgggagctttcaattccgactattttaaaaaattattgtgcttttttctgcatgtcatatttcacacttgccttattgttcgacagGTACTTTGATGCTATTGTTCATATGGATATGAGCTTGCATTCAATGGAAGTAGTAAATCGGCTCACTACTGCAGTAGTTTTACCACCAGGATTTGTTCAT

upper sequence: LOC_Os11g13694.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G133757_T01 (Zea mays), 3'ss of exon 9
gtatgtagattagccttgtcgtttattctattgttttcttatttaattactaatttactatgtttctctactcacaacgtcttactcacatgcctttttctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT
|||   | | ||||||| || | | || |||  || || | | |||||| |       |   ||| ||| |   | |  | | ||  || |||||| || ||  |||| |||||||||  | |||| || ||||| |||||| | |||||||||||||| ||||||||||||||||| ||||||| | |||||||||||||  |||| 
gtacacatactagccttttcatctgttttatctttatcct-tgtaattattg------tgcttttttctgcatgccagatttcac--acttgccttattgttcaacagATACTTTGATGCTATTGTCCATATGGATATGAGCTTGCATTCAATGGAAGTAGTAAACAGGCTCACTACTGCAGTAGTTTTACCACCAGGATTTGTTCAC

upper sequence: LOC_Os11g13694.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G00610.3 (Glycine max), 3'ss of exon 9
gtatgtagattagccttgtcgtttattctattgttttcttattta-attactaatttactatgtttctctactcacaacgtcttactcacatgcctttttctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT
||||| |  ||  |  | |  | |  ||| | | |||  ||  || ||| |    |  ||||  || |||  | |     |  || |  | |   | |   |   |||| |||||     | |||||  | ||||| ||||| |||||||||||||||||||| |||||||| || |||||||| || |||||  |   ||||||||| 
gtatgcatttttcctctattatattatctgt-gctttagtacatacattgccctatcgctattattttct--ttat----ttctatttgcttatttatggat---acagATACTTCACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTTACAACAGCAGTTGAACTACCGTCTCAATTCATTCAC

upper sequence: LOC_Os11g13694.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 9
gtatgtagattagccttgtcgtttattctattgttttcttattta-attactaatttactatgtttctctactcacaacgtcttactcacatgcctttttctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT
||||| |   |  |  | |  | |  ||| | | | |  ||  || |||||    |  ||||  || |||  | |     |  || |  | |   | |   |   |||| ||||||    | |||||  | ||||| ||||| |||||||||||||||||||| |||||||| || ||||| || || |||||| |   ||||||||| 
gtatgcattcttcctctattatattatctgt-gctctagtacatacattaccctatcgctattattttct--ttat----ttctatttgcttatttatggat---acagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC

upper sequence: LOC_Os11g13694.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgtagattagccttgtcgtttattctattgttttcttatttaattactaatttactatgtttctctactcacaacgtcttactcacatgcctttttctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT
                 ||   | ||    || ||   |     | |||||  |  || |   || |  |||   || ||   | ||  | |  |  |||||   ||| || | |||   ||| |   | ||||| |||||||| || |||||||||||||| || |||||||| || ||||| || || ||    |  ||||| |  
-----------------gtaagtcatcaccttattggttccaccatttactt-tcgaccaaaattata-acttttaaagtgggaatc-taagaatgcttctt---cagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG

upper sequence: LOC_Os11g13694.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv07s0130g00310.t01 (Vitis vinifera), 3'ss of exon 9
gtatgtagattagccttgtcg-tttat-tctattgttttcttatttaattactaa------------tttactatgtttctctactcacaacgtcttactcacatgcctttttctttgacagTT-----ACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT
||||||   || | | ||| | ||||  | | ||| ||| ||| | || |  |||            |||| | | ||||| |  |      || ||  |    | | || || |||| || ||     ||||     |||||||    ||||| ||||||||||||||||||||||| || |||||||| |||||||| || || || ||  | | |||  | || 
gtatgtt--tttgtcatgttgatttacctttcttgctttattactgaaatgataagcatcccagcactttaatctttttcttttttttttctgtatttttgctttcctttcttttttgtcaatttagGTACTTCAGAGTTCTTGTCAGTATGGACATGAGCCTACATTCAATGGAAGTCGTTAACAGGCTTACTACAGCGGTTGAACTTCCCACCGAATTTGTACAC

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|29620671|gb|CB625682.1|CB625682
EST:     GTTGCTGTTGAAGTCCTTTCAAAGTTAATCAACTCGCCTGACATGGATGC                         TTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGT
genomic: GTTGCTGTTGAAGTCCTTTCAAAGTTAATCAACTCGCCTGACATGGATGCgtatgtagat ... tctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGT




















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: 51 (upstream exon), 63 (downstream exon)
Score: 11

GACCTTGTGGAACATAATCCACTCGTTGCTGTTGAAGTCCTTTCAAAGTTAATCAACTCGCCTGACATGGATGCgtatgtagat ... tctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactatgtttctctactcacaacgtcttactcacatgcctttttctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT
                             tactcac  putative branch site (score: 11)
                                   catgcctttttcttt  CT-rich tract
                                         tttttcttt  TA-rich tract