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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacaattctgaactgcgaaactttacattatagtatcgtttatcactactttattagggtatgtgaaacatgtcagctgatcatttgcaaaaattttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGACAGTAAGGAGGTTGCCAAGGCTCAGAAAAAGAAGAAGGCGATGTTTTGCT

Basic information

species Oryza sativa
transcript LOC_Os02g04020.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G073571_T01 (Zea mays), 3'ss of exon 13
-----------------------------------------------------------------gtaaacaattctgaactgcgaaactt-tacattatagtatc-gtttatcactactttattagggtatgtgaaacatgtcagctgatcatttgcaa-----------------aaattttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGACAGTAAGGAGGTTGCCAAGGCTCAGAAAAAGAAGAAGGCGATGTTTTGCT
                                                                 | | || |  |  ||   ||  |  | || || | ||| |  | || |   |  |||  |  | |     |      |||||      ||| | |                  || |||| | ||||  | || |||||||||||||||||||||||||| || ||  |||||||||| |||||| |||||| |||||||                         
gtaacattttattaattaagcgcgcaatagtagcacgtggttttgcttcttgcttttgcataccagcatactacgcaaaagctcgtcatgtatatataaaagtttttgcttgtttgtggtttgattagcttcagcagtttcatcagccagctgtttactatgcatcatcttatctgtgaaatttccctagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTCGCGAACATCGACAGCAAGGAGATTGCCAGGGCTCAG-------------------------

upper sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G171354_T01 (Zea mays), 3'ss of exon 13
-------------------------------------------------------------------gtaaacaattctgaactgc--gaaactttacatta--tagtatcgtttatcactactttattagggtatgtgaa----acatgtcagctgatcatt---tgcaa----aaattttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGACAGTAAGGAGGTTGCCAAGGCTCAGAAAAAGAAGAAGGCGATGTTTTGCT
                                                                   | |||   |  | |  |||  | |  || |  | |  ||| ||  |||    || ||| |||||  |     |     ||    |||||| ||||    |||       || ||||   ||||  | || |||||||||||||||||||||||||| || || ||||||||| | || ||| ||||||||||||||                         
gtaatcttttgttaattgccggacatggtttttcttctttcttttccatataatgccagcctactttgcaaaagctcgtcatgtgcctgtagattaagttcacttaggattattt--tgcttcttgattagctttcagcagtttcaccgtccagctgctcatcacatgcgtttctgaaatttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG-------------------------
















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|88380611|gb|CI521180.1|CI521180
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|89167705|gb|CI021404.1|CI021404
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88536302|gb|CI466046.1|CI466046
EST:     CTGTCCNCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|25801464|gb|CA757425.1|CA757425
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|87021095|gb|CI271902.1|CI271902
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|58031064|gb|CX728607.1|CX728607
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|9864991|gb|AU100741.1|AU100741
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88527413|gb|CI455571.1|CI455571
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88552331|gb|CI481007.1|CI481007
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|87020904|gb|CI269621.1|CI269621
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88275769|gb|CI396373.1|CI396373
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|66914754|gb|CX101602.1|CX101602
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88531618|gb|CI458478.1|CI458478
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88559947|gb|CI490567.1|CI490567
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|29640360|gb|CB645369.1|CB645369
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|29686150|gb|CB682425.1|CB682425
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88544986|gb|CI472515.1|CI472515
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88552294|gb|CI480967.1|CI480967
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88440461|gb|CI549342.1|CI549342
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|86260767|gb|CI000215.1|CI000215
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|29625319|gb|CB630330.1|CB630330
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88539011|gb|CI468083.1|CI468083
EST:     CTGTCCGCCCTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88560113|gb|CI490745.1|CI490745
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88528368|gb|CI456526.1|CI456526
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
EST: gi|88528467|gb|CI456708.1|CI456708
EST:     CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAG                         GCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC
genomic: CTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGAC

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: 71 (upstream exon), 70 (downstream exon)
Score: 61

AGATAAGCCTTCAGAGATGCCCTGCGAGAAAGAAGAGTTGCTTAATGCTGCTGTCCGCCGTGTGGATGCGCTGGAAGCTGAACTTATTGTAACAAAGAAGgtaaacaatt ... ttttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGACAGTAAGGAGGTTGCCAAGGCTCAGAAAAAGAAGAAGGCGATGTTTTGCT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttattagggtatgtgaaacatgtcagctgatcatttgcaaaaattttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGACAGTAAGGAGGTTGCCAAGGCTCAGAAAAAGAAGAAGGCGATGTTTTGCT
                          agctgat  putative branch site (score: 61)
                                             ttttctc  putative PPT
                                  atttgcaaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacaattctgaactgcgaaactttacattatagtatcgtttatcactactttattagggtatgtgaaacatgtcagctgatcatttgcaaaaattttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGACAGTAAGGAGGTTGCCAAGGCTCAGAAAAAGAAGAAGGCGATGTTTTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG