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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtcagccatggacgcggaattcccatctgcctctacctctctccccccctccccctctcctgcgccggccccccggtgttctagggtttcggtg...

Basic information

species Oryza sativa
transcript LOC_Os07g07240.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G022206_T02 (Zea mays), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtcagccatggacgcggaattcccatctgcctctacctctctccccccctccccctctcctgcgccggccccccggtgttctagggtttcggtg------------------------------------------------------------------------------------
||||||||||||||| ||| |||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||     ||| ||||   | | ||   |||  |  || |    ||  |    ||| | ||   ||  | |   |     | | ||||  |   || || |                                                                                    
TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgta--cctcatccatcc-cacagagccccccac--cccccgagtccgttaatcccgctcctgttctagggtttgattgacag-gttccggatcttgggggggtgagaaacgggttctcatctattcctttccattttcactcgtgtttgttgtgctgatgagagaggttcgtttgattttgcag

upper sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G074479_T04 (Zea mays), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtcagccatggacgcggaattcccatctgcctctacctctctccccccctccccctctcctgcgccggccccccggtgttctagggtttcggtg-----------------------------------------------------------------------------------------------------
||||||||||||||| ||| |||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| |       ||       |    | |||   |  |  |||| | |   | ||| |||      | |      |||     |||||||||||||   ||                                                                                                     
TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtcccctcccctcccccctcccccgatttcgttaccccacaaacgccccccctggagtccgt-taatcccgttcctgttctagggtttgattgagggactccggatctcggggagggagacgggatctcagctattccttttgttcttactcttgtgttcgttgtgctgatgagaggttcgtgtggtttcgcag

upper sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtcagccatggacgcggaattcccatctgcctctacctctctccccccctccccctctcctgcgccggccccccggtgttctagggtttcggtg----
||||||| ||||||||||| |||||||| || || || || || ||||||||||| ||||| ||||||||||||||| | ||||| || ||||| |||||||      ||  | |   | | || || |  ||||| |   |   | |  |    |          | ||  || | |   |  ||  | ||    |  |    
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgta---cccaaac-tcctccccgattttcgttctgcatgctcaattgtgtcggtatgaatgcgaaattcgtggggcgcggagatttgcatggcggtgtcggttt

upper sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtg--ggtgt-cagccatggacgcggaattc--ccatctgcctctacctctctccccccctccccctctcctgcgccg-gccccccggtgttctagggtttcggtg
||||||| |||||||||||  |||| || || || || || || ||||||||||| ||||| |||||||| |||||||| ||||| || || || |||||||   |  || |  || |||   ||   ||    ||  ||  ||      |    |    | | ||   | || |  | || |  ||| ||    |  ||      
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaacgaagtgcctccctggtttcgttttttgttcaattgtgtccggtcgtggtgcggaattcgccgggcgtgggaggcgcacgtcggagtgtcggtttt------

upper sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtcagccatgga---cgcggaattcccatctgcctctacctctctccccccctccccctctcctgcgccggccccccggtgttctagggtttcggtg
||||||| || |||||||| || ||||| || || || || || ||||||||||| || || |||||||| |||||| | ||||| || || ||||||||||| ||    || |       |   |  ||      || |  | | |   | |                                                  
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcgaaacctttcttagggtttttgaatgtcggttctttcttacag------------------------------------------------

upper sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgt-cagcca-tggacgc-ggaattcccatctgcctctacctctctccccccctccccctctcctgcgccggccccccggtgttctagggtttcggtg
||||||| ||||||||||| || || || || || |||||||| ||||||||||||||||| |||||||||||||||||||||||||| || |||||||||| ||  |  ||||  | | | |  |  |  | ||||  ||||   | ||      |                                              
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcggcactagggtatcgatctaactcttggtttcgtgttgcag--------------------------------------------

upper sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgt-cagcca-tggacgc-ggaattcccatctgcctctacctctctccccccctccccctctcctgcgccggccccccggtgttctagggtttcggtg
||||||| ||||||||||| || || || || || |||||||| ||||||||||||||||| |||||||||||||||||||||||||| || |||||||||| ||  |  ||||  | ||| |  |  |  | ||||  ||||   | ||      |                                              
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaactcttggtttcgtgttgcag--------------------------------------------

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|58589089|gb|CF987397.1|CF987397
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|88370680|gb|CI592446.1|CI592446
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|33829483|gb|CF340565.1|CF340565
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|87018548|gb|CI252302.1|CI252302
EST:     CATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: CATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|58589326|gb|CF987634.1|CF987634
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|396941349|gb|HO188558.1|HO188558
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|58602468|gb|CK012996.1|CK012996
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|58594410|gb|CF992718.1|CF992718
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|86601347|gb|CI251721.1|CI251721
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|58597267|gb|CK007795.1|CK007795
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|88390727|gb|CI610953.1|CI610953
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|86592637|gb|CI253318.1|CI253318
EST:     GCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|15008457|gb|AU222845.1|AU222845
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|86599452|gb|CI251410.1|CI251410
EST:     AACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: AACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|33661350|gb|CF292317.1|CF292317
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|88826116|gb|CI776681.1|CI776681
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|88727870|gb|CI749382.1|CI749382
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|88364559|gb|CI612374.1|CI612374
EST:     GGCGCGCCGAACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|218486911|gb|FG967738.1|FG967738
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|88571683|gb|CI663056.1|CI663056
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|3767492|gb|AU031602.1|AU031602
EST:     NCGCCCGCACGACAACCAACATTCATGCTCTGGAACGCCGTCATCTTCGG                         CCCGGATGATACCCCTTGGGACGGAG
genomic: GCG-CCGCACGACAA-CAACA-TCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|27577517|gb|CB000212.1|CB000212
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|88721800|gb|CI745099.1|CI745099
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|88444098|gb|CI594471.1|CI594471
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|88440712|gb|CI693273.1|CI693273
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|33823815|gb|CF337714.1|CF337714
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|218500131|gb|FG955693.1|FG955693
EST:     TGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: TGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|87023876|gb|CI288229.1|CI288229
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|55409265|gb|CV721641.1|CV721641
EST:     GTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG
EST: gi|7608720|gb|AU090501.1|AU090501
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGG                         GCCGGATGATACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG

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: 74 (upstream exon), 68 (downstream exon)
Score: 159

TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtca ... tgttttgcagGCCGGATGATACGCCGTGGGACGGAG




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