Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgtttccaattactgtcatcctacattactgcttgctctcttgccacctacttgctatttgtcctttgcactttgcagaccttttctctgt...

Basic information

species Oryza sativa
transcript LOC_Os05g50840.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g50840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G067877_T02 (Zea mays), 5'ss of exon 3
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgtttccaattactgtcatcctacattactgcttgctctcttgccacctacttgctatttgtcctttgcactttgcagaccttttctctgt--------------
||||||| |||||||||||||| ||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| ||||| || |||| || ||   || ||| ||||||||     | ||  ||    | || |||  | |||| | | | || ||| |       | ||||||||| ||||||| ||              
CAGAGGGCCTCCGTGGACTTTTCAAGGGCAATGGTACCAATTGTGCAAGGATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTACGAGCAGGCGTCAAAgtatgcccttttttgcaattact-----cttaagttgt--cctgttctgctaccacttgcctactgtttat-------agtttgcagacattttctcggttgcattgcatgatt

upper sequence: LOC_Os05g50840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA19G44300.1 (Glycine max), 5'ss of exon 3
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgtttccaattac--tgtcatcctacattactgc--ttgctctcttgccacc-tacttgctatttgtcctttgcactttgcagaccttttctctgt
| || ||| | ||||| || || || || |||||||| ||||||||  ||||||| ||||||||||| |||||||| || || ||||||||||| || | ||  | | |  |||  |  |||  ||   | || || |  |    |       |||  |   |   | ||      | |||  | |||    |  |||| ||   
CTGAAGGTTTTCGTGGGCTGTTCAAAGGGAATGGTACTAATTGTGCTCGAATTGTCCCAAATTCTGCTGTGAAGTTCTTCAGTTATGAGCAAGCTTCCAAgtaagctttcctttagatatacactgatgtactgcacttttatgatgataaatttgtaatgatggattctgccatccttttttatttt----attttttttcaa-

upper sequence: LOC_Os05g50840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA11G02090.1 (Glycine max), 5'ss of exon 3
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgtttcca-attactgtcatcctacattactgcttgctctcttgccacctacttgctatttgtcctttgcactttgcagaccttttct-ctgt-----
| |||||| |  | ||| | ||||| || || || || ||||||||  | || || |||||||| || |||||||| ||||||||||||||||| || | || || |    | |||| ||| || |  |  ||  ||  |  ||||||| ||   |  |  ||  | ||  ||  |  | || |  | |   ||  | ||       
CTGAGGGTTTTAGAGGAATGTTTAAAGGAAACGGAACAAATTGTGCTCGTATAGTCCCAAATTCAGCAGTGAAGTTCTTTAGCTATGAGCAAGCTTCCATgtatgct----tctccacatttctattctgatatttttttcattgctctgttttaaatttgttaat-ttaatcagtctccctctaaatatgcttaatactaatgcag

upper sequence: LOC_Os05g50840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA03G41690.1 (Glycine max), 5'ss of exon 3
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgtttccaattac--tgtcatcctaca-ttac-----tgcttgctctctt-gccacctacttgctatttgt---cctttgcactttgca---gaccttttctctgt----------------------------
| || ||| | ||||| || || || || |||||||| || |||||  ||||||| ||||||||||| |||||||| || || ||||||||||| || | ||  | | |  |||  |  |||  ||   | || || |||      || |  |||  || |||   || || | |||| |    |  || | |    |    ||  ||||||                               
CTGAAGGTTTTCGTGGGCTGTTCAAAGGAAATGGTACTAACTGTGCGCGAATTGTCCCAAATTCTGCTGTGAAGTTCTTCAGTTATGAGCAAGCTTCCAAgtaagctttcctttagatatacattgatgtactgcacttataaacatggtcactcctttcgcctagtagtttcaatttttatatccatgtattacatatgtaacactttctcctctttttactgactgttccttttctggcag

upper sequence: LOC_Os05g50840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA16G03020.1 (Glycine max), 5'ss of exon 3
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgttt-----ccaattactgt-catcctacattactgcttgctctcttgccacctacttgctatttgtcctttgcactttgcagaccttttctctgt
| || ||  ||||||||||||| || || |||||||| |||||||| |||||||| || |||||||| |||||||| || || ||||||||||| || | ||  ||| || |||     | ||  | ||| |   ||  |||| || ||  | ||||   |     ||| | ||  | |   |    |   | |||   |  |   
CTGAAGGATTCCGTGGACTTTTCAAAGGGAATGGTACTAATTGTGCTAGAATTGTCCCTAATTCTGCTGTGAAGTTCTTCAGTTATGAGCAAGCTTCTAAgtaagtttttctttagatacaaaacaatgtgcggactgtattattgtttagtatcttttta-----ttggttttcattcagggggactattataccaaataccaa-

upper sequence: LOC_Os05g50840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G06410.1 (Glycine max), 5'ss of exon 3
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgtttccaattactgtcatcctacattactgcttgctctcttgccacctacttgctatttgtcctttgcac--tttgcagaccttttctctgt
| || ||  | ||||||||||| || || |||||||| |||||||| |||||||| || |||||||| || ||||| || || ||||||||||| || | ||  ||| || |||  |   |     ||   |    ||||| |  |   ||   | ||  ||| |  || || || |      |   | |||   |  |  |
CTGAAGGATTTCGTGGACTTTTCAAAGGGAATGGTACTAATTGTGCTAGAATTGTCCCTAATTCTGCTGTTAAGTTCTTCAGTTATGAGCAAGCTTCTAAgtaagtttttctttagatacaaaacaatgtgagg--actgccttattgtttagtatctttttgtttgttttcattcgggggactattataccaaatgccaat

upper sequence: LOC_Os05g50840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA01G43380.1 (Glycine max), 5'ss of exon 3
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgtttccaattactgtcat-cctacattactgct-tgctctcttgccacctacttgctatttgtc-ctttgcactttgcagaccttttctctgt--------
| |||||| |  | ||| | ||||| || || || || ||||||||  | ||||| |||||||| || |||||||| ||||||||||||||||| |||  ||  | |  |         || | | ||   ||  | | |||| |||| |          | ||  |||  ||| |  | ||  |   | |  |  |   |          
CTGAGGGTTTTAGAGGAATGTTTAAAGGAAACGGAACTAATTGTGCTCGTATTGTCCCAAATTCAGCAGTGAAGTTCTTTAGCTATGAGCAAGCTTCACTgtaggcttctccacatttgtattctgatatttatttcattgctctgctttaaatttgttaatttaatatcagtctccctccaaataataaatatgcttaatactaatgcag

upper sequence: LOC_Os05g50840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G01100.1 (Arabidopsis thaliana), 5'ss of exon 3
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgt------ttgttattgtttccaattactgtcatcct-acattactgcttgctct---cttgccacctacttgctatttgtcctttgcactttgcagaccttttctctgt---
| ||||| || |||||||| || || || ||||| ||||| |||||  | |||||||| ||||| || || || ||||| |||||||||||||| |||| ||      |   |||  | ||      |||| ||| | |  ||| |    ||      ||||  ||       || ||| |  | |   ||||       ||||||||     
CCGAGGGACTTCGTGGACTGTTCAAAGGAAATGGCACCAACTGTGCTCGTATTGTTCCTAATTCGGCTGTTAAATTTTTCAGCTATGAGCAAGCTTCAAAgtaagacatctatatcttctctgtactctgttatcttgatcttaataaaggcatcatacttgatactatagatctttttctaatctatgctttttctcttttttctctcatag

upper sequence: LOC_Os05g50840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G01100.2 (Arabidopsis thaliana), 5'ss of exon 3
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgtttccaattactgtcatcctacattactgcttgctctcttgccacc-tacttgctatttgtcctttgcactttgcagaccttttctctgt
| ||||| || |||||||| || || || ||||| ||||| |||||  | |||||||| ||||| || || || ||||| |||||||||||||| |||| ||  |  ||  | |    |  |||| |  ||    |  || |     |   | || | |||||| || |                                
CCGAGGGACTTCGTGGACTGTTCAAAGGAAATGGCACCAACTGTGCTCGTATTGTTCCTAATTCGGCTGTTAAATTTTTCAGCTATGAGCAAGCTTCAAAgtaagacatc-tatatcttctctgt-actctgttatcttgatcttaataaaggcatcatacttgatactatag----------------------------

upper sequence: LOC_Os05g50840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv02s0025g01180.t01 (Vitis vinifera), 5'ss of exon 3
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgtttccaattactgtcatcctacatt---actgcttgctctcttgccacctacttgctatttgtcctttgcactttgcagaccttttctctgt
| |||||| |||| ||||| ||||| |||||||| |||||||||||| | ||||| |||||||| || || ||||| | ||| |||||||||||||| | ||  ||| |  | | |    | | |||   |  |||   || || |    |  |   || |||| |    |||  | |    |  || |      ||      
CTGAGGGTTTCCGGGGACTATTTAAAGGCAATGGAACCAATTGTGCCCGCATTGTACCAAATTCAGCAGTCAAGTTCTATAGTTATGAGCAAGCATCCAAgtacgttttcctattcttaaagtttcagtattgatttcaacagcgtcagtttattttacatactggtgccttgcacatgtatccctgaatggtcattgaa---

upper sequence: LOC_Os05g50840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S84_131V6.1 (Physcomitrella patens), 5'ss of exon 3
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgtttccaatta----ctgtcatcctacatt---actgcttgctctcttgccacctacttgct--atttgtcctttgcactttgcagaccttttctctgt------------------------------------------------------------------
  || ||  | |||||| |||| ||||||||||| || ||||||||| | ||  |||| |||||||| |||||||||||    |||||  |||| || | || ||| |   |   ||||||    |  | || || |||    |  ||    | |  | | ||  |     |  || | |  | ||   | || |  | ||| |    |                                                                  
GCGAAGGGATACGTGGATTTTTCAAGGGCAATGGCACTAATTGTGCCCGGATCATTCCCAATTCTGCTGTGAAGTTTTTCGCTTATGAAGAAGCGTCCAAgtgtgtaacc-tcagcaattaaactcctttatactgcatgtggagggccgtgtttagtactactgagagattcgatcttttttgtgtggtctgaaatcttttgcaggatctttatcagatgagctttcacattctgttgtgattttcattgtatgggttttcttttatttggcag

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|29636411|gb|CB641420.1|CB641420
EST:     ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|29615469|gb|CB620481.1|CB620481
EST:     ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|29662184|gb|CB658459.1|CB658459
EST:     ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|426174|gb|D22033.1|D22033
EST:     ATTGTTCCAAATTCTGCCGNNAAGTTTTTTAGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|58690108|gb|CK078795.1|CK078795
EST:     ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|29622345|gb|CB627356.1|CB627356
EST:     ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|33796657|gb|CF324196.1|CF324196
EST:     ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|29616138|gb|CB621150.1|CB621150
EST:     ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|25802905|gb|CA758866.1|CA758866
EST:     ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCANG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|88298517|gb|CI563512.1|CI563512
EST:     TTGTNTC-AAATTCTGCCGTGAAGTTTTT-AGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAAACAA-CAGGGAATG
genomic: TTGT-TCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAA-CAAACAGGGAATG
EST: gi|38474124|gb|CF958256.1|CF958256
EST:     ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|27577139|gb|CA999833.1|CA999833
EST:     AAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: AAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|29615006|gb|CB620019.1|CB620019
EST:     ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG
EST: gi|218493719|gb|FG966455.1|FG966455
EST:     ATTGTTCCAAATTCTGCCGTGAAGTTTTTTACCTATGAGCAAGCATCAAG                         TGGAATTTTATGGCTTTATCGGCGACAAACAGGGAATG
genomic: ATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG

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: 70 (upstream exon), 73 (downstream exon)
Score: 57

CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttatt ... ttttatgcagTGGAATTTTATGGCTTTATCGGCAACAAACAGGGAATG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAGGGTCTCCGTGGACTTTTTAAGGGCAATGGTACCAATTGTGCCAGAATTGTTCCAAATTCTGCCGTGAAGTTTTTTAGCTATGAGCAAGCATCAAGgtttgttattgtttccaattactgtcatcctacattactgcttgctctcttgccacctacttgctatttgtcctttgcactttgcagaccttttctctgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG