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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttagcttttttgacaacatggatgtctaattctttatgtctggtgtctaacatccatattgtgtattcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAGTAAGAGGTTTTCATGACGTGGAACACAACACCAAGCCTAGTCGCTAGTC

Basic information

species Oryza sativa
transcript LOC_Os02g52140.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G143163_T01 (Zea mays), 3'ss of exon 2
gtaagtttagcttttttgacaacatggatgtctaattctttatgtctggtgtctaacatccatattgtgtattcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAGTAAG-AGGTTTTCATGACGTGGAACACAACACCAAGCCTAGTCGCTAGTC
|||||| | | |  | |   |   |  ||||  | ||||    || |  | |||||| |    || || |||  || | |||||| |  || | ||||||||| || ||||||||||| |||||||| ||||||| | | |   | || | ||  ||  ||| ||||  | | ||   | || 
gtaagtattg-tggtgtactactgtcaatgtggatttct---agttttctttctaacgt---aatcgtttatcgttttgcagGAGGGCTCCTACATTCCGCCGCCCTATGCGCTACAGACCATACTTCTGAAGTACGTACGGGGTAATAATGTTCAATGCAAAACCAGTCATGGTTAGTGGT-
















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|88487256|gb|CI424527.1|CI424527
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|86854695|gb|CI258986.1|CI258986
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|86258520|gb|CI064873.1|CI064873
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|32948090|gb|BP184662.1|BP184662
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGGTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|87024798|gb|CI261307.1|CI261307
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88482866|gb|CI420137.1|CI420137
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|87025376|gb|CI267742.1|CI267742
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88517174|gb|CI444510.1|CI444510
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCNCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|86544962|gb|CI185168.1|CI185168
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|86491058|gb|CI133691.1|CI133691
EST:     TACCAATATAGATCGTATGGGGCCCAATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|87018233|gb|CI265525.1|CI265525
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88483997|gb|CI421268.1|CI421268
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88847474|gb|CI015967.1|CI015967
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|66926559|gb|CX113407.1|CX113407
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|86505168|gb|CI147801.1|CI147801
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|86417997|gb|CI032206.1|CI032206
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88506260|gb|CI433766.1|CI433766
EST:     TATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCNCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88492082|gb|CI429354.1|CI429354
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88519815|gb|CI447469.1|CI447469
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCNCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|58598948|gb|CK009476.1|CK009476
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTATGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88505737|gb|CI433243.1|CI433243
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88554840|gb|CI485049.1|CI485049
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88473106|gb|CI410377.1|CI410377
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|86255584|gb|CI065261.1|CI065261
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|33664620|gb|CF295587.1|CF295587
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88222758|gb|CI220823.1|CI220823
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88255030|gb|CI353854.1|CI353854
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88478290|gb|CI415561.1|CI415561
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88469773|gb|CI407044.1|CI407044
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|87032407|gb|CI264188.1|CI264188
EST:     TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88491850|gb|CI429122.1|CI429122
EST:     TATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
EST: gi|88980934|gb|CI021061.1|CI021061
EST:     TACCCATATAGATCGTATGGGACCCCATATTTCCCACCATATGGTTACGG                         GAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG
genomic: TACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttag ... tcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtctaattctttatgtctggtgtctaacatccatattgtgtattcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAGTAAGAGGTTTTCATGACGTGGAACACAACACCAAGCCTAGTCGCTAGTC
                       gtctaac  putative branch site (score: 2)
                                            ttcttgttc  putative PPT
     taattctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttagcttttttgacaacatggatgtctaattctttatgtctggtgtctaacatccatattgtgtattcttgttcagGAGAGTCCCCAGATTCCGCCGTCCAATGCGCTACAGGCCATACTTTTGAAGTAAGAGGTTTTCATGACGTGGAACACAACACCAAGCCTAGTCGCTAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG