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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcccggatcgatcgatcgatcgagatttgtactgatttggttggttctgatttgtgttgggatttgggtgcag

Basic information

species Oryza sativa
transcript LOC_Os01g15010.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G122666_T01 (Zea mays), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtag-----gtcgcccggatcgatcgatcgatcgagatttgtactgatttggttggttctgatttgtgttgggatttgggtgcag--------------------
|||||| ||||| |||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||         | ||   |||   |  |    |  |     | | |  ||   || ||  || ||     ||  |   | |   |                    
GCTGGCATCGCTTGGGCTGTGGCAGAAGGAGGCTAAGATCCTCTTCCTTGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTGAAGGACGAGgtcctctctacctccgacatccgccccttttccttgcgaattccagtcttatatgctttcgacttaacggggattcctgatctggttcgattgggttcatcgcag

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA10G28910.1 (Glycine max), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcc-cggatcgatcgatcgatcgagatttgtactgatttggttggttctgatttgtgttgggat--ttgggtgcag-------------------
 ||||| ||||| ||| ||||||||||||||||||||||| | ||| | || ||||| || ||||| ||||||||| | || ||||||||||| ||||||||    |    | | |  | |  |  ||||   |||  | | | | ||   ||| |  |||  ||| | ||  ||  || ||                    
TCTGGCATCGCTTGGGTTGTGGCAGAAGGAGGCCAAGATCTTATTCTTAGGTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttttccgcttaagccctgaatcgc--tttaaatttactgggaatgttattcttttagttagaatccttttgtacaatttaaatattattacgaga

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA19G41670.1 (Glycine max), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtag-gtcgcccggatcgatcgatcgatcgagatttgtactgatttggttggttctgatttgtgttgggatttgggt-gcag
 || || ||||| ||||||||||||||||||||||||||| | ||| | |||||||| ||||| ||||| || ||| | || ||||||||||| || |||||   ||   ||   |   |   |   ||   | | ||  |   ||  ||  || | |||  | |  |  || |  | ||||
TCTAGCGTCGCTCGGGCTGTGGCAGAAGGAGGCCAAGATCTTATTCTTGGGCCTCGATAACGCTGGCAAAACTACCTTGCTTCACATGCTCAAAGATGAGgttttgttttccttttttttttttgtttccccaatcgt-ttaccttttttttttattattattataagagttggttttgcag

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA03G39110.2 (Glycine max), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcccggatcgatcgatcgatcgagatttgtactgatttggttggttctgatttgtgttg-ggatttgggtgcag---------------------
 || || ||||| || |||||||||||||||||||||||| | ||| | |||||||| ||||| ||||| |||||| | || ||||||||||| || |||||    | |    ||   |    |  |     | | | |  | ||| ||  |  || ||| | ||  ||||| |     ||                     
TCTAGCGTCGCTTGGCCTGTGGCAGAAGGAGGCCAAGATCTTATTCTTGGGCCTCGATAACGCTGGCAAAACCACCTTGCTTCACATGCTCAAAGATGAGgtt--cctcttcaatttcttttcccttttttttgtttccccaattgtttaatattgttttttcttttggattcgttaatagtggtggatctgcccttatttg

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA20G38360.1 (Glycine max), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcccggatc-------gatcgatcgatcgagatttgtactgatttggttg-gttctgatttgtgttgggatttgggtgcag-------------
 ||||| ||||| ||  ||||||||||||||||||||||| | ||| | || ||||| || ||||| ||||||||| | || ||||||||||| ||||||||    |   |  |||       | |   |     |    || | |  |   | ||  |  |||| | |  ||   ||||    | |              
TCTGGCATCGCTTGGATTGTGGCAGAAGGAGGCCAAGATCTTATTCTTAGGTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttccctttcccatccttttccgcttatttctctgctccttcttcacaaacgcttaagccctgaatcg-atttaaatttactgggaatcttattcgttta

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S183_17V6.1 (Physcomitrella patens), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtagg----tcgcccggatcgatcgatcgatcgagatttgta-ctgatttggtt---ggttctgatttgtgttgggatttgg-gtgcag-----------
||| ||| |  | ||| | ||||||||||||||||| ||| | ||||||||| | ||||||||||||||||||||  | || |||||||||||||| |||||  |     ||   |   | |  ||| | | |||||    | | | |||  ||   || |  |   |||| |||| |||   ||  |            
GCTTGCCACCTTAGGGTTATGGCAGAAGGAGGCCAAAATCTTGTTCCTCGGCTTGGACAACGCCGGCAAGACCACGTTGCTGCACATGCTCAAGGATGAGgtgagggctccgtttgctcccaaggatagttagagatggagagcgggtttcattcacgggttgggactgtgctgggctttcttgtttattgttaaatttc

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S7_338V6.1 (Physcomitrella patens), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgta------ggtcgcccggatcgatcgatcgatcgagatttgtactgatt-tggttggttctgatttgtgttgggat----ttgggtgcag---------
||| ||  |  | ||||| |||||||||||||| || ||||| ||||||||| | || ||||| |||||||||||  | || |||||||||||||| ||||||      ||    || | | ||  ||   |  ||     | |  ||     |    ||   |   |  ||| |||    | | |||| |         
GCTTGCGACCTTAGGGCTATGGCAGAAGGAGGCGAAAATCCTGTTCCTCGGCTTGGATAACGCGGGCAAGACCACGTTGCTACACATGCTCAAGGATGAGgtaagggctggcttaccagctagaaggaagaaaggaaggaaggaaggagggcagggaatttataaacggcttgagatagtttcgtgtgctgtgttgtttc

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S10_357V6.1 (Physcomitrella patens), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcccggatcgatcgatcgatcgagatttgtactgatttggttggtt-ctgatt-tgtgttgggatttgggtgcag--------------------
 || ||     | ||||||||||||||||||||||| ||||| || || || |||||||| || |||||||| || || || |||||||||||||| |||||  | | | |   ||  |   | |||      |||  |   ||   || |    ||||   ||       ||| |   |                      
TCTTGCGAGCATAGGGCTGTGGCAGAAGGAGGCCAAAATCCTGTTTCTGGGTCTCGACAATGCTGGCAAGACTACTCTTCTGCACATGCTCAAGGATGAGgttagactctcttttctgtt--ttgattcctgcttggtcaatttcaattcgcggttgatagcgtaccaaattttcgcctctagaatcgataacgtatccgtt

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S44_58V6.1 (Physcomitrella patens), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgc---ccggatcgatcgatcgatcgagatttgtactgatttggttggttctgatttgtgttgggatt--tgggtgcag---------------
 || ||     | ||  ||||||||||||||||||| ||| | ||||| || || ||||| ||||| ||||| || || || |||||||||||||| |||||    | |   || |||   |    |  |      || |        | |||   |||  |   | | | | |   || | | |               
TCTTGCGAGCATAGGTTTGTGGCAGAAGGAGGCCAAAATCTTGTTCCTGGGTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctccccttgccagatttcttctccttttttttcttttttcccacggtttgtgcctggctgccgctagaaatgtcggtttctgtcttcatggcttctg

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ35155 (Selaginella moellendorffii), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcccggatcgatcgatcgatcgagatt-tgtactgatttggttggttctgatttgtgttgggatttgggtgcag--------------------------
| ||||| |||| |||||||||||||||||||||||||| |||||||| || |||||||| || || || || || || |||||||||||||||||||||||  || |     | |   |  | || |   ||   || ||||    |    |   |     | ||  | |||   | |                            
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagagctccatcgcgttctgaggccgcctctctcgcgcgctcttttggttttttttctttttttcttttctcgcaattcttccag

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ16976 (Selaginella moellendorffii), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcccggatcga-tcgatcgatcgagatttgtactgatttggttggttctgatttgtgttgggatttgggtgcag
  | ||    || ||||||||||||||||||| ||||||| | ||||| || |||||||||||||||||||| || || || ||||||||||||||||||||| |         | || |       || || |    |  ||| |||  || |      || |  |              
CTTAGCGAGCCTAGGGCTGTGGCAGAAGGAGGGCAAGATCTTGTTCCTAGGGCTCGACAACGCCGGCAAGACGACGCTGCTACACATGCTCAAGGACGAGgtaagcgaatttcttggaatttcctcctctaggtc---atggatctgg--ggattgcgcctgcgcag--------------

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ12822 (Selaginella moellendorffii), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcccggatcgatcgatcgatcgagatttgtactgatttggttggttctgatttgtgttgggatttgggtgcag
  | ||    || ||||||||||||||||||| ||||||| | ||||| || |||||||||||||||||||| || || || ||||||||||||||||||||| |         | ||     |   |     |  |   ||| |||  || |      || |  |              
CTTAGCGAGCCTAGGGCTGTGGCAGAAGGAGGGCAAGATCTTGTTCCTAGGGCTCGACAACGCCGGCAAGACGACGCTGCTACACATGCTCAAGGACGAGgtaagcgaatttcttggaatttcctcccctaggtcatg--gatctgg--ggattgcgcctgcgcag--------------

upper sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgc--ccggatcgatcga----tcgatcgagatttgta-ctgatttggttgg------ttctgatttgtgttgggatttgggtgcag---------
| ||||| |||| |||||||||||||||||||||||||| |||||||| || |||||||| || || || || || || |||||||||||||||||||||||  || |   || | |    | |    || |||| | | ||   | |  |   |||       || || ||| |  |    |||    |||          
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag

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|33662007|gb|CF292974.1|CF292974
EST:     GCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAG                         CGGCTCGTGCAGCACCAGCCGACGCAGTACCCGACGTCGGAGGAGCTGAGC
genomic: GCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcc ... ttgggtgcagCGGCTCGTGCAGCACCAGCCGACGCAGTACCCGACGTCGGAGGAGCTGAGC
EST: gi|55412880|gb|CV725256.1|CV725256
EST:     GCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAG                         CGGCTCGTGCAGCACCAGCCGACGCAGTACCCGACGTCGGAGGAGCTGAGC
genomic: GCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcc ... ttgggtgcagCGGCTCGTGCAGCACCAGCCGACGCAGTACCCGACGTCGGAGGAGCTGAGC
EST: gi|38565812|gb|CK085265.1|CK085265
EST:     GCCTCGACAATGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAG                         CGGCTCGTGCAGCACCAGCCGACGCAGTACCCGACGTCGGAGGAGCTGAGC
genomic: GCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcc ... ttgggtgcagCGGCTCGTGCAGCACCAGCCGACGCAGTACCCGACGTCGGAGGAGCTGAGC
EST: gi|58685384|gb|CK074071.1|CK074071
EST:     GCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAG                         CGGCTCGTGCAGCACCAGCCGACGCAGTACCCGACGTCGGAGGAGCTGAGC
genomic: GCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcc ... ttgggtgcagCGGCTCGTGCAGCACCAGCCGACGCAGTACCCGACGTCGGAGGAGCTGAGC

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: 64 (upstream exon), 55 (downstream exon)
Score: 22

GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcc ... ttgggtgcagCGGCTCGTGCAGCACCAGCCGACGCAGTACCCGACGTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAGGCCTTCGACCTCGGCGGCCACCAGATCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgcccggatcgatcgatcgatcgagatttgtactgatttggttggttctgatttgtgttgggatttgggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC