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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgatattctcttaatggttctcaccgcaagtgattaaactagtcaaataatgtttctcatttcctcttaccagatgaatcagatcttgtgagatt...

Basic information

species Oryza sativa
transcript LOC_Os08g06480.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g06480.1 (Oryza sativa), 5'ss of exon 21
lower sequence: Vv16s0039g02410.t01 (Vitis vinifera), 5'ss of exon 21
TGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgatattctcttaatggttctcaccgcaagtgattaaactagtcaaataatgtttctcatttcctcttaccagatgaatcagatcttgtgagatt-
||| || |||||  | || ||||| |||||||| |||||||||||||| || ||||||||||| ||||| |||||||| ||||||||  | ||||| |||||||   || |  | ||  || ||       |  ||| ||  | | || |||      ||||   |||   |     |||||       | | ||   || 
TGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcat-tgtttttgttgattaatttttcctgtgtttttaattgttaaagtcaaattctatcttcaagtggaatgatgatgtcttgcatatgcttttt

upper sequence: LOC_Os08g06480.1 (Oryza sativa), 5'ss of exon 21
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
TGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgat---attct--cttaatggttctcacc---gcaagtgattaaactagt--caaataatgtttctcatttcctcttaccagatgaat-----cagatcttgtgagatt----------------
 || || ||||| |||||||| || || |||||||| |||||||||||||| |||||||| || || || ||||| ||||||||||| ||||| || |||||  || ||    | ||  |   ||   |  | |    |  | |  | | ||| ||    |   || | ||||  ||  |  ||  |||           |    |  | |||||                
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcggttt-taatataagactgtcgttgatacgcttaataagatttctctgctgttcacag

upper sequence: LOC_Os08g06480.1 (Oryza sativa), 5'ss of exon 21
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 21
TGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtg--------agtgatattctcttaatggttctc---accgcaagtgattaa-actagtcaaataatgtttctcatttcctcttaccagatgaatcagatcttg-tgagatt-----
 || || ||||| ||||| ||||| || |||||||| || |||||||| || ||||||||||| || || || || ||||||||||| ||||| || |||||          |   |  | ||||  || |   |   |||     |||||   | | ||||  |  | ||    ||  |   | |   |   ||| ||| |||  ||   ||     
AGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAATACAGATTTATAATGTTCGTGTAGATGAGgtattttaccaggccgttctttctttgtgatctcccgtacctatgttgatttgtattcgtcagtttgtattctagatcccgaataatgtgcctaattagagctttctgctgttggcag

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|58683700|gb|CK072387.1|CK072387
EST:     TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAG                         GTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
genomic: TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgata ... tatggcatagGTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
EST: gi|33793091|gb|CF322427.1|CF322427
EST:     TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAG                         GTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
genomic: TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgata ... tatggcatagGTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
EST: gi|58596216|gb|CK006744.1|CK006744
EST:     TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAG                         GTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
genomic: TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgata ... tatggcatagGTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
EST: gi|58687154|gb|CK075841.1|CK075841
EST:     TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAG                         GTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
genomic: TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgata ... tatggcatagGTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
EST: gi|58667666|gb|CK056352.1|CK056352
EST:     TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAG                         GTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
genomic: TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgata ... tatggcatagGTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
EST: gi|27577716|gb|CB000411.1|CB000411
EST:     TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAG                         GTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
genomic: TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgata ... tatggcatagGTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
EST: gi|58608562|gb|CK036595.1|CK036595
EST:     TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAG                         GTTAAAAGCAAGCTTAAGGGACATGCAAAAAAGATCACTGGGCTGGCATTT
genomic: TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgata ... tatggcatagGTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
EST: gi|58674933|gb|CK063620.1|CK063620
EST:     TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAG                         GTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT
genomic: TTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgata ... tatggcatagGTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTT

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: 68 (upstream exon), 73 (downstream exon)
Score: 70

TGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgata ... tatggcatagGTTAAAAGCAAGCTTAAGGGACATTCAAAAAAGATCACTGGGCTGGCATTTTCGCAGTCAATGAATATGCTTGTATCTTCAGGTGCTGATGCTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgatattctcttaatggttctcaccgcaagtgattaaactagtcaaataatgtttctcatttcctcttaccagatgaatcagatcttgtgagatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA