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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactccatcatcttacctttccatttctcatggttatggtggatgatcttttaactgttatatatacttttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os11g28340.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g28340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G031802_T01 (Zea mays), 5'ss of exon 2
TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactccat-catcttacctttccatttctca----tggttatg----gtggatgatcttttaactgttatatatactttt-gttgcag-----------------------------------------------------
||| ||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| || || |||||||||||| | ||| |    | | | |||  ||| ||      || ||  |    |   || || |  | |  | | | |  |||     ||   |                                                     
TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattccttgtgccatccatttttattccttgaatgtgattcggagccgcacattatttcattaaagatgtttgcactccccattatggtaggtgtaaccgttattcatgcagccattttctttgtgtttttcttaacccag

upper sequence: LOC_Os11g28340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G35390.1 (Glycine max), 5'ss of exon 4
TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactcca-tcatcttacct------ttccatttctcatggttatgg---tggatgatcttttaactgttatatatacttttgttgcag--------
 |||||| | |  || || || || |||||||||||||| ||||| || ||||| || || || |||||||||||||||   | |  | ||  |   |      | | |||| |  || || |     |  |  |  | ||||||  | | |  | | ||      |        
-GCATACAGAGCACTATACATTCTCAACTGGATCTACCGCTACTTTACCGAGCCTCACTTTGTCCATTGGATAAGtatgattttctcttattctgtttaatggttactattttttttgcttctacacttaaaataattattaactactctctgcattgttaactatgtcttgtgg

upper sequence: LOC_Os11g28340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G46570.1 (Glycine max), 5'ss of exon 4
TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatgga-ctccatcatcttacctttccatttctcatggttatggtgg-atgatcttt-taactgttatatatacttttgttgcag--------------
||||||| | |  || || || || ||||||||||| || ||||| ||||||||||| || || |||||||||||||||   |||  | ||  |   ||    || ||  |  || || |   | | |  || ||| | |||  ||         ||||               
TGCATACAGAGGACTATACATTCTCAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattctctcttattgtgttttatggttactattttttttgcttctacgcttattataattattaagtaactacactctgcattattcactactatg

upper sequence: LOC_Os11g28340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G25040.1 (Arabidopsis thaliana), 5'ss of exon 4
TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactccatcatctt---acctt---------tccatttctcatggttatggt-ggatgatcttttaactgttatatatacttttgttgcag----
 |  |||||||   | || ||||| |||||||||||||| |||||||||||||| || || ||||| ||||||||||||  |  |    |||    |||||         ||  ||| |  |  |  |  | |||| |  ||||  |   |||    |||| ||    |     
GGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGAGCCGCACTTTGTTCACTGGATAAgtatgttcctctctctctctcaaccttcactgagcatctgtttattttcctcctaattggattagtttttgtcaactattgcaacttatgactaaaaatg

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|88476998|gb|CI414269.1|CI414269
EST:     AGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: AGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88849104|gb|CI087626.1|CI087626
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88555052|gb|CI485279.1|CI485279
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88528582|gb|CI456828.1|CI456828
EST:     CGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: CGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|86542052|gb|CI182258.1|CI182258
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|86529172|gb|CI169378.1|CI169378
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|426840|gb|D22915.1|D22915
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|86886118|gb|CI321154.1|CI321154
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|27546640|gb|CA764760.2|CA764760
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88262756|gb|CI366530.1|CI366530
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GGTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|86870391|gb|CI319497.1|CI319497
EST:     GATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGGCTGACTTCTTCTAC
genomic: GATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTAT-GCTGACTTCTTCTAC
EST: gi|88533140|gb|CI460677.1|CI460677
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88241404|gb|CI241253.1|CI241253
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88541507|gb|CI470782.1|CI470782
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|33691459|gb|CF319698.1|CF319698
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|86545642|gb|CI185848.1|CI185848
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88529756|gb|CI458100.1|CI458100
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|89187774|gb|CI009758.1|CI009758
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88439304|gb|CI536276.1|CI536276
EST:     TACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT

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: 74 (upstream exon), 64 (downstream exon)
Score: 44

TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG




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