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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accaccacatgcatctttctggctggcttagtcagcctatgaaagccatatactggattcacatatcttataatacctcctaactattttcacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGCATTGGTGTCATTCAG

Basic information

species Oryza sativa
transcript LOC_Os05g42330.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 10
accaccacatgcatctttctggctggcttagtcagcctatgaaagcca-tatactggattcacatatcttataatacctcctaactattttcacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGCATTGGTGTCATTCAG
||| | | | | | | | | | | | ||| ||| | | |||| | || ||| ||| |||||||||||||| || || ||||| || ||||||||||| ||||| |||||||| ||||||||||||
-tcactctttaccaatcgacgctacatccaataatcatgtattggttggcatagcttatttagttcctaagtaatttactgtttctttttatgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGCATCGGTGTCATTCAG

upper sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 10
accaccacatgcatctttctggctggcttagtcagcctatgaaagccatatactggattcacatatcttataatacctcctaacta------ttttcacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGCATTGGTGTCATTCAG
| | ||||| || | | | || | || |||||| ||| || ||| ||| || | |||| || || || |||||||||||||| || || || || || ||||||||||| ||||| |||| || ||||||||||||
--aaaaaaatgcactcttt--accaattgtcgctgcatccagtagtcatatattgg-ttgggatagctt-cgttaggttctaagtaattgaccttgtgtctgacagATATTTTACTTCGTTGGATTCGGCTTGTTCTGCCTTGAATCACTTATGAGTATCGGTGTCATTCAG

upper sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 9
------------------accaccacatgcatctttctggctggcttagtcagcctatgaaagc--------catatactggattcac----atatcttataatacctccta-actattttcacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGCATTGGTGTCATTCAG
|| || | | |||| | ||| || | | || | ||||| | |||| | || || ||| || | ||| | | |||||| | |||||| | |||||||| || |||||| |||| ||||||||||||||| | || ||||||
gtaagtaccaattgtgttactactattttttggcttctaattta-ttattctccttccaaagggaggggttatatatattcatgtcacgatgacatgtttaaatcataccaatacttgtcctgaattacagATACTCTACTTTATTGGGTTTGGTTTTTTCTGCATTGAATCACTGCTGAGCATTTGGGTTATTCAG

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|86831256|gb|CI297525.1|CI297525
EST:     CATAGGCAGGAGTGCTATAGTGGGG                         ATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
genomic: CATAGGCAGGAGTGCTATAGTGGGGgtaagtatct ... cacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
EST: gi|88964067|gb|CI032984.1|CI032984
EST:     CATAGGCAGGAGTGCTATAGTGGGG                         ATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
genomic: CATAGGCAGGAGTGCTATAGTGGGGgtaagtatct ... cacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
EST: gi|33803682|gb|CF327716.1|CF327716
EST:     TGGGATTTTGCCTGCCATTGATGTCATAGGCAGGAGTGCTATAGTGGGG                         ATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
genomic: TGGGATTTTGCCTGCCATTGATGTCATAGGCAGGAGTGCTATAGTGGGGgtaagtatct ... cacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
EST: gi|89188347|gb|CI115596.1|CI115596
EST:     AGGAGTGCTATAGTGGGG                         ATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
genomic: AGGAGTGCTATAGTGGGGgtaagtatct ... cacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
EST: gi|86595040|gb|CI260279.1|CI260279
EST:     CTGGGATTTTGCCTGCCATTGATGTCATAGGCAGGAGTGCTATAGTGGGG                         ATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
genomic: CTGGGATTTTGCCTGCCATTGATGTCATAGGCAGGAGTGCTATAGTGGGGgtaagtatct ... cacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
EST: gi|58686999|gb|CK075686.1|CK075686
EST:     TGGGA-TTTGCCTGCCATTGATGTCATAGGCAGGAGTGCTATAGTGGGG                         ATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
genomic: TGGGATTTTGCCTGCCATTGATGTCATAGGCAGGAGTGCTATAGTGGGGgtaagtatct ... cacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
EST: gi|33803684|gb|CF327717.1|CF327717
EST:     CTGGGATTTTGCCTGCCATTGATGTCATAGGCAGGAGTGCTATAGTGGGG                         ATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
genomic: CTGGGATTTTGCCTGCCATTGATGTCATAGGCAGGAGTGCTATAGTGGGGgtaagtatct ... cacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
EST: gi|4881016|gb|AU065315.1|AU065315
EST:     TGGGATTTTGCCTGCCATTGATGTCATAGGCAGGAGTGCTATAGTGGGG                         ATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC
genomic: TGGGATTTTGCCTGCCATTGATGTCATAGGCAGGAGTGCTATAGTGGGGgtaagtatct ... cacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGC

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: 61 (upstream exon), 60 (downstream exon)
Score: 35

TGGGATTTTGCCTGCCATTGATGTCATAGGCAGGAGTGCTATAGTGGGGgtaagtatct ... cacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGCATTGGTGTCATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatatactggattcacatatcttataatacctcctaactattttcacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGCATTGGTGTCATTCAG
                                tcctaac  putative branch site (score: 35)
 ttttcactt  putative PPT
 acatatcttataata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accaccacatgcatctttctggctggcttagtcagcctatgaaagccatatactggattcacatatcttataatacctcctaactattttcacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGCATTGGTGTCATTCAG

- - - acatgca
- - - - - - - - - -tggctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gattcac