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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataacatatccattgctgatgcatttatggactctttattctattttattgtgtttatatgtacaaatacacataatctctatgctatctaacacattcttactgttctatcttcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCGGTGCTCTTTGTCATGAACACAATGTGGTTTATGAAGATCTTGAAAGGCG

Basic information

species Oryza sativa
transcript LOC_Os03g46410.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G132084_T04 (Zea mays), 3'ss of exon 9
gtaataacatatccattgctgatgcatttatggactctttattctattttattgtgtttatatgtacaaatacacataatctctatgctatctaacacattcttactgttctatcttcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCGGTGCTCTTTGTCATGAACACAATGTGGTTTATGAAGATCTTGAAAGGCG
||| ||| || | |||| |  ||| ||||||           ||| ||| |     | ||||  | ||| || | ||  ||| | |    |            | | |    |   |    | ||| |||||||||||||||| |||||||||||| |||| ||| |||||||||||||||||||||| ||||||||||||||||| ||||||||||| |||||||
gtactaagatcttcattccaaatgaatttat-----------tctgtttaaaaa-atatatac-ttcaagtataaatg-tctttgtctcgttg----------tgccgcctgacacttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACGTTTGTTGTGCCATCGGTGCTCTTTGTAATGAACACAATGTGGTTCATGAAGATCTTAAAAGGCG

upper sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G132084_T02 (Zea mays), 3'ss of exon 8
gtaataacatatccattgctgatgcatttatggactctttattctattttattgtgtttatatgtacaaatacacataatctctatgctatctaacacattcttactgttctatcttcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCGGTGCTCTTTGTCATGAACACAATGTGGTTTATGAAGATCTTGAAAGGCG---------
||| ||| || | |||| |  ||| ||||||           ||| ||| |     | ||||  | ||| || | ||  ||| | |    |            | | |    |   |    | ||| |||||||||||||||| |||||||||||| |||| ||| |||||||||||||||||||||| ||||||||||||||||| ||||||||||| |||||||         
gtactaagatcttcattccaaatgaatttat-----------tctgtttaaaaa-atatatac-ttcaagtataaatg-tctttgtctcgttg----------tgccgcctgacacttaactacagataatgcagATGCATGCCTTTGGGTACTACCTGACGTTTGTTGTGCCATCGGTGCTCTTTGTAATGAACACAATGTGGTTCATGAAGATCTTAAAAGGCGTGATGAAAA

upper sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G016184_T02 (Zea mays), 3'ss of exon 8
gtaataacatatccattgctgatgcatttatggactctttattctattttattgtgtttatatgtacaaatacacataatctctatgctatctaacacattcttactgttctatcttcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCGGTGCTCTTTGTCATGAACACAATGTGGTTTATGAAGATCTTGAAAGGCG
||| ||| || | |||| || ||||||||||      | | || ||     || |  | |  |||| |  ||       ||| | |||  ||| |||| |   |||                  || |||||||||||||||| |||||||||||| |||||||| |||||||||| ||||||||||| ||||||||||||||||| ||||||||||| ||||| |
gtactaagatcttcattcctaatgcatttat------tctgttttacaaatttatagtcaactgtaaaggtatttgcc-tctttgtgccgtctgacacttaactac------------------agATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCAGTGCTCTTTGTAATGAACACAATGTGGTTCATGAAGATCTTAAAAGGTG

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|33681072|gb|CF309311.1|CF309311
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|86852608|gb|CI321728.1|CI321728
EST:     GACTTCTGTTCAGGTACGTATTCTATCACATCTATATGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTAGTTGTGCCATC
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTA-TTGTGCCATC
EST: gi|86415587|gb|CI029598.1|CI029598
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|86261100|gb|CI004665.1|CI004665
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCAGTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|11025554|gb|AU162155.1|AU162155
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|86494039|gb|CI136672.1|CI136672
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|3763019|gb|AU029771.1|AU029771
EST:     CACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: CACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|89187704|gb|CI115150.1|CI115150
EST:     TCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|86259320|gb|CI007997.1|CI007997
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG

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: 66 (upstream exon), 28 (downstream exon)
Score: 7

GTTGCAAGGATACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCGGTGCTCTTTGTCATGAACACAATGTGGTTTATGAAGATCTTGAAAGGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacataatctctatgctatctaacacattcttactgttctatcttcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCGGTGCTCTTTGTCATGAACACAATGTGGTTTATGAAGATCTTGAAAGGCG
                            ttcttac  putative branch site (score: 7)
                            ttcttactgttctatc  CT-rich tract
                 tatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataacatatccattgctgatgcatttatggactctttattctattttattgtgtttatatgtacaaatacacataatctctatgctatctaacacattcttactgttctatcttcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCGGTGCTCTTTGTCATGAACACAATGTGGTTTATGAAGATCTTGAAAGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA