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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt...

Basic information

species Oryza sativa
transcript LOC_Os01g23610.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G145595_T02 (Zea mays), 5'ss of exon 4
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaa-cacatgcatagaaa---cagacatgtt--ttgggtgcatacatgttctgcaagtgtcttttcttggctt
||||||||||||||||||||| ||||| ||||||||||| || ||||| |||||||||||||| |||||||||||||||||||| ||||| |||||||||||| ||||||| |   | |    |||||||   |||  |||||| |||  |    |  | ||||  ||   |      || |||  |     | | |  |      
TGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGATGTATACACAGCTCTAGGAAGTGAGgtatatgaacaatcattcaagc-catcattgcttaaatacatgcttagggagtctaatcgtgttagttattttagcgaatattcctctgtcatatatcatg-----

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgc--atagaaacagacatgttttgggtgcatacat--gttctgcaagtgtcttttcttggctt-------------------------------------------------------------------------------------------
|||||| ||||| ||| | |||||||| ||||| || || || ||||| ||||| ||||| || ||||||||||||||||| ||||| || ||||||||||||   | ||   || |  |||  ||  |||| || |   |    || | |         |     |  |  |||   ||| | ||| | |  |||  || | |                                                                                           
TGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGATGTATATACGGCCCTTGGAAGTGAGgta---gtacttctcttctgatatatttttttttatcctttctcaattgtattttgttcatgagaagaactgacaatagttttccaatttttcttttatgacgtttgaaagttttttatattatctcattgtttgaaaagttagaaacctaatttgtgcagaagagatatagttggtaataatggtactctgcag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G37050.2 (Glycine max), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt-
 ||||| ||||| || || |||||||| ||||| || || || ||||| || || ||||| || ||||||||||||||||| || || || ||||||||||||     |   ||   ||  |  ||  ||||        |    |  | |     |  ||  |    ||  |         | |    |   ||| | | 
CGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGATGTATATACAGCACTTGGAAGTGAGgta-gcacatctttgtgaattttgatactttttctttctcttttcattaccttttgttcttgagaaatatttacaaataatcaatcctatcatttgacatc

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt--------
 ||||| ||||| ||||| |||||||| ||||| || || || ||||| || || ||||| || ||||||||||||||||| || || || ||||||||||||   | ||| |   |  |||  |   |||  |      | |||   | |     |  ||       ||  ||          |  |||   ||| | |        
CGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGATGTATATACAGCACTTGGAAGTGAGgta---gcaca-tctttgtgat--actgtttctttcttttttcatt--accttttgttcttgataaatatttataaataatcgatcccttcatttgacatcagaaata

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgta-catgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt--
|||  | ||| | ||||| || ||||| |||||||| || || ||||| ||||| ||||| || || ||||||||||| ||||| ||||| |||||||||||| |||||    |   ||  |   ||  |  | ||  ||   | | |  |  |   |||  | | | | |     |     || ||   ||       ||  
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatgatattactttagtacg-actttgtgat-gttgtgtccttg-tacttgagattgtaataactgcaattagcaatgttct

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaaca-gacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt------
|||| | ||| | ||||| ||||||||||||||||| || || ||||| ||||| || || || || ||||||||||| |||||||| || ||||||||||||     ||| ||   |   ||    | |   |  |||  |  |   |    |   | ||||| || | |   |  | | |   | ||| |   | |         
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgta-----aca-ttttgattttgtgctaatgatttgcactggtgtgatagtgtgttgttttttgcgttc-tctttagttttctgttttctctcaatagtaacaaaag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgtt-ctgcaagtgtcttttcttggctt-
||| || ||||| ||||| |||||||| ||||| || || || ||||| ||||| ||||| || |||||||||||||| || || || || ||||||||||||         ||  ||         |||       | ||  ||| |||  || |  |||             ||| | ||     |||  |  |    | 
TGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAGgta-gcatcttctttatagtcattgcgattacagtttaaatttatataaat-gagaaatttcaatcaatagtgagttacagcttagatctggtgctaaaatc

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgt-tctgcaagtgtcttttcttggctt---------------------
||| || || || ||||   | || ||||||||||| || || ||||| ||||||||||| || || ||||| ||||| || || || || |||||||||||| |     | |||||     |||| |||     |||     ||| ||   ||  |||   | | |  |  |  | ||||  | |   |     || |||                     
TGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGATGTCTATACTGCCCTTGGAAGTGAGgtaaa-----atttccttg--cgcattatt----gacaataaaataaaagtggatgtgtggagtgcgtgtgtaattatctgacaataattggagctgacttcccttttctgtgggcttgcag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagtt--cctaagat------gcatcatt-ttctaacacatgcatagaaacagac--atgttttgggtgcatacatgttct-gcaagt-gtcttttcttggctt-------
 ||  | ||  | ||||   |||| ||||||||||| ||||| || |||||||||||||| || || ||||||||||||||||| ||||| ||||| |||||   | | |  ||  |  | | |      ||||  || || ||    ||   |  |    | |  || | ||     | |  |||  ||  ||||| | | | | || |          
CGCTTTGAAGTTAGAGTGGATTCCAGACTGGATTGCGATCGTTGGCAGCGGTTACATTGGTCTAGAGTTCAGTGATGTATACACAGCTCTCGGAAGCGAGgtcagtaaccgtttgtctcacggtctaggagcatttttattttattctattttttcactttgtcgtatatcttcatcacttgtatggactcacaagttgacctcttttcgtgcccggcag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcataca--tgt--tctgcaagtgtcttttcttggctt---------------
|||  | || || ||||   |||| ||||||||  |||| || ||||| ||||||||||| || || ||||||||||| ||||| || || ||||| |||||||| |     ||   | ||  ||  |||||  || | |   || || | |     ||| | | |  | | |  |||  |||    | |  | || |   |||               
TGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGATGTTTACACTGCCCTTGGAAGCGAGgtaca-gttttattgaaaggacacaatatttttaaaaata-aaatggatatat-tgggttctagttttaaaaagttgtcatctagtggagcttattttcctcttgctgtgggttggcag

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|58684178|gb|CK072865.1|CK072865
EST:     GTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAG                         GTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCT
genomic: GTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaac ... acttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCT




















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: 60 (upstream exon), 75 (downstream exon)
Score: 24

TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaac ... acttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT




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