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'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagtttcttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG

Basic information

species Oryza sativa
transcript LOC_Os03g52840.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 6
---------tgagtttc--ttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG-------
         ||| |  |  || ||| | |||||||||| |  ||||||||| ||||||| | |||||        | || ||| |   |||| || |  ||    ||||||||||| ||||||||||| || |||  ||| ||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||||       
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactc--------ctatagctcaaaggttctacctactg---tttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGGTCATTT

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
---------tgagtttc--ttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
         ||| |  |  || ||| | |||||||||| |  ||||||||| ||||||| | |||||        | || ||| |   |||| || |  ||    ||||||||||| ||||||||||| || |||  ||| ||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||||
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactc--------ctatagctcaaaggttctacctactg---tttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 6
tgagtttcttccccctcaattcttagttatgt--tcagatat---aatgctcttggtactctcatcctcc-catggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
  |   |||  |   |  ||| | | | ||||    || | |   ||| | ||| | |   ||||  ||  |||    || |  | | ||| ||       ||||||||||||| || ||||| || ||||| |||||||| |||||||||||||| ||  ||||| ||||||| || || |  || || ||||| |||
acaagctctatcagttgtattttaattcatgtaacaagctctctcaattcacttagcatcttcattatctgcatctaatattgctgctactacta------tgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 6
tgagtttcttcccc--ctcaattcttagttatgttcagatataatgctct-tggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
 |  |||| |   |  |||   |   |  | | || |  | ||    | | ||  |   || |  |  || |  |   ||| | |  |  |||     |||||||||| || |||||||| || || || || ||||||||||| |||||||| ||||||||| |||| |||||||| |  || |||||||| |||
agcctttcattagcaactccccttgcacctcttttaaattgtagcaatgtgtgccatattctttgtaacaagatt---ttgattatttgtttgtatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 6
-----------tgagtttcttccccct---caattcttagtt-atgttcagatataatgctcttg--gtactctcatcct-cccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
             ||| |||    | |   || |   || || |  |||   | | ||    |||  | | |   ||  |  |  |  || | || ||  | ||  |  ||  |||||||||| || ||||| || || || || || || || |||||||||||||| |||||||||||||| | |||||| |  ||||||||||| |||
gtacttgggttctagtctctctagcttggtcagtcagtatttgactttcttttctcatctctttgtggaattgatattgtatcttttcctcatttcttttatttgctcttg--tgcagACTGACACGAAGAAAATATCGGCTGTATCCATCTTTTTTGAGACAATGCCATACAGATTGGATGAGAACACTGGTTACATTGATTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 3'ss of exon 6
tgagtttcttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggctta-gttgttcaacttcttgatggttg-cagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
                    |   |||||  ||   || | |   | | || ||||||   |||  |||  | |   | |    ||||||  |  |   |||||||| || |||||||| ||||| || || || |||||||| ||||||||||| |||||||| || ||||||||||  || || || ||||||
---------------gtgccttcaagttaactttgtatgtca---tttcggaactctctgactctgatgaataacagtttctttcttcttatttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCCTATAGATTGGACGAGAGCACTGGCTACATCGACTACGATCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0211g00160.t01 (Vitis vinifera), 3'ss of exon 6
tgagtttcttccccctcaattcttagttatgttca-gatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatggt-tgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG-------
   ||||||      | |     |     ||||   | ||| ||   ||| |   ||| ||   |    |  | |  |  |||  |  | | |  | ||||||| || || ||||| || || ||||| || ||||| |||||||||||||| || |||||| |||| ||||||||||  ||||| ||||| |||       
-aggtttctaatatttgatgatctctccttgtttgtggtattat-tactttgccttcttatgtgctagggagtaacctcctcatttcttcgctattgtgcagACCGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAGGTAACTT

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 6
tgagtttcttccccctcaattcttagttatgttca-gatataatgctcttggtactctcatcctcccatggc--ttagttgttcaacttcttgatggt-tgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
   ||||||      | |     |     ||||   | ||| ||   ||| |   ||| ||   |    | |  | |  |  |||  |  | | |  | ||||||| || || ||||| || || ||||| || ||||| |||||||||||||| || |||||| |||| ||||||||||  ||||| ||||| |||
---gtttctaatatttgatgatctctccttgtttgtggtattat-tactttgccttcttatgtgctagggacagtaacctcctcatttcttcgctattgtgcagACCGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 6
tgagtttcttccccctcaattcttagttatgttca-gatataatgctcttggtactctcatcctcccatggc--ttagttgttcaacttcttgatggt-tgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
   ||||||      | |     |     ||||   | ||| ||   ||| |   ||| ||   |    | |  | |  |  |||  |  ||| |  | |||||||||| || ||||| || || ||||| || ||||| |||||||||||||| || |||||| |||| ||||||||||  ||||| ||||| |||
---gtttctaatatttgaggatctctccttgtttgtggtattat-tactttgccttcttatgtgctagggacagtaacctcctcatttctttgctattgtgcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 6
---tgagtttcttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatgg----ttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
   ||||         | ||  | |||  || | ||  |||| || |||     |    |||   ||  |||   ||| | |||| | |  |  |      |||||||| || || |||||||| || || || || ||||| |||||||||||||| ||||||||||||||||  ||||| |  ||||| ||||| |||
atttgaggaataatttcttct-tcctttttttttttttgata-aaagct-----tgtcttcagtatctgatgtgctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S21_270V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------------------tgagtttcttccccctcaat-tcttagttatgtt--cagatataatgc-tcttggtactctcatcctc--ccatggcttagttg----ttcaacttcttgatggttg-cagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
                                               |  |||  ||   || ||| || ||     |||  ||    || | | | |  | ||  |  ||| |   ||||  ||  ||     ||||   | || ||||    ||||||||||| |||||||||||||| ||||| || ||||| ||||| |||||||||||| || | ||   ||| || |  || || |||||||||
gtacgtcttctggttttctattcatgcccaatttatacttgcttgtggtatttgctcaaactgaatatcctaagatggttgccattcttactacgtatctgcacgtttctccacaatcatgaatttattcacacttcatgcttttcatggcaaacagACTGATACAAAGAAGATTTCAGCCGTTTCCATTTTCTTCGAGACTATGCCCTACAGACTGAACGAGTCCACAGGTTATATCGACTATGATCAG

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|29674139|gb|CB670414.1|CB670414
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|38472219|gb|CF956350.1|CF956350
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|58691585|gb|CK080272.1|CK080272
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|29672938|gb|CB669213.1|CB669213
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|25798315|gb|CA754276.1|CA754276
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|38472528|gb|CF956660.1|CF956660
EST:     TCATGGC-TTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|58661735|gb|CK050415.1|CK050415
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|84117692|gb|CD285458.1|CD285458
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|38471655|gb|CF955786.1|CF955786
EST:     CTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: CTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|33800499|gb|CF326119.1|CF326119
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|29681405|gb|CB677680.1|CB677680
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|29681406|gb|CB677681.1|CB677681
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|58689542|gb|CK078229.1|CK078229
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|14571290|gb|BI118658.1|BI118658
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|58692794|gb|CK081481.1|CK081481
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|58609394|gb|CK037427.1|CK037427
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|29674038|gb|CB670313.1|CB670313
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
                                        tcttgat  putative branch site (score: 4)