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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatcacttacacccataccaatcataaattaagaatttattattacagcttatatatactattatcatgcatgtatattatctaaaaaa...

Basic information

species Oryza sativa
transcript LOC_Os07g37920.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G179885_T02 (Zea mays), 5'ss of exon 1
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatcacttacacccataccaatcataaattaagaatttattattacagcttatatatactattatcat--gcatgt--atattatctaaaaaa
|| || ||||||||||||||||||||||| ||||| || ||||||||| |||||||||| |||||||| ||||||||||||||||| ||||| || || |||||||||  ||        ||   || ||   |||| |  |     ||   |       | ||  |||  ||  | ||  |||||   || | |||| |    
GTCGTCCACTACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaaggtagcgcgcgccatatatgccg-ccatatac-atatcctttccaacgtgattgatgaatataatatttattggcatggtgatctcatcttact--

upper sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G179885_T04 (Zea mays), 5'ss of exon 2
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatcacttacacccataccaatcataaattaagaatttattattacagcttatatatactattatcat--gcatgt--atattatctaaaaaa-------
         |||||||||||||||||||| ||||| || ||||||||| |||||||||| |||||||| ||||||||||||||||| ||||| || || |||||||||  ||        ||   || ||   |||| |  |     ||   |       | ||  |||  ||  | ||  |||||   || | |||| |   |       
---------TACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcgccatatatgccg-ccatatac-atatcctttccaacgtgattgatgaatataatatttattggcatggtgatctcatcttactcattctgct

upper sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA13G35560.1 (Glycine max), 5'ss of exon 1
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatcacttacaccca---------taccaatcataaattaagaattta-------ttattacagcttatatatactattatcatgcatgtatattatctaaaaaa--------------------------
|| || |||||||||||||| || || || || | ||| || || ||  |||||||||||||||| |||||||||||||||||||| ||||| || ||||||| ||  || |||  | | || | |         | | ||   ||  || | || | |       || ||  |  || ||| |  ||||||      | | ||||   ||  |                            
GTAGTTCACTACCTCAAGAAAAAAGCAGCTTCTGCTCCTCTTCCGGTAGCCATCATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttcttcaatttcatccaacgaatcaaaagattcaaactttacgttcaaaactcaaatgggtttgttttactttttattttgtattatttactttttgtatttattatgatttttctttatttttgtgtggttggcag

upper sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA12G34990.1 (Glycine max), 5'ss of exon 1
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatcacttacacccataccaatcataa-attaagaatttattattacagcttatatatacta---ttatcatgcatgtatattatctaaaaaa-------------------------------
||||| |||||||||||||| ||  | || || | ||| || || ||  |||| ||||||||||| |||||||||||||||||||| ||||| || ||||||| ||  || ||| | || || ||| || ||||| || ||| | | || |   | | | || | ||         || |  |   | | ||||||    |  |                               
GTGGTTCACTACCTCAAGAAAAAAACAGCTTCTGCTCCTCTTCCGGTAGCCATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttcttcaattaatttcatcca-acgaatcaaaagattcaaacttcacgttcaaaactcaaatgggtctgctttgttttttttatttattattattatgatttttctttatattttgtttgtggttaacag

upper sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA15G07620.1 (Glycine max), 5'ss of exon 1
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatcac-ttacacccataccaatcataaattaa---gaatttattattacagctt-atatatacta--ttatcatgcatgtatattatctaaaaaa-------------------------------------
||||| |||||||||||||  || || | ||| ||||| || || ||  |||||||||||||||| ||||||||||||||||| || ||||| |||||  ||| | || || |||||    || |  | |   || |   || |    ||   | | | | |  |  ||   || |   ||| | |  || ||| || |  |   ||                                     
GTGGTTCACTACCTCAAGAGAAAAGCAGACTCTGTTCCTCTTCCTGTTTCCATCATCGCCGAGGTTGATCTCTACAAGTTCGACCCATGGGAACTCCCAAgtatgcaacttcatcacaccccaacttttcttttcctcctttcatgcaaacccact-tcatatttccatgcttaattgcttaccttatatttattttttggatccaatattttcatttttgactttttttgtgtttttttttag

upper sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA07G31220.1 (Glycine max), 5'ss of exon 1
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatcacttacaccc-ataccaatcataaattaagaatttat-tattacagcttatatatactattatcat-gcatgtatattatctaaaaaa
||||| |||||||||||||  || || || || |  || || |||||| ||||||||||||| || ||||||||||||||||| || ||||| |||||  ||| |   | || |   | |||||| ||   |    |  ||  |   || |  ||| |  | ||  |  |    |    ||  ||  ||| || | |  | | 
GTGGTTCACTACCTCAAGAGAAAAGCTGCTTCTGCACCCCTTCCCGTCGCCATCATCGCCGATGTTGATCTCTACAAGTTCGACCCTTGGGAGCTCCCAAgtatgc--tctactttatcacaccccattttatctttccatccatttttcaaatatcaaggttttaaattgtggtagctatcacaattatgttcttttgata-

upper sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA13G31660.1 (Glycine max), 5'ss of exon 1
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatcactta--cacccataccaatcataaattaa---gaatttattattacagcttatatatactattatcatgcatgtatattatctaaaaaa--------------------------------------------------
||||| || ||||||||||| || || | ||| ||||| || || ||  |||||||||||||||| |||||||||||||| || || ||||| |||||  ||| | || || |||||  |  ||||  | |   || |   || |    ||   | | |      ||  ||     |||      | | |  |     | ||                                                     
GTGGTTCAGTACCTCAAGAAAAAAGCAGACTCTGTTCCTCTTCCTGTTTCCATCATCGCCGAGGTTGATCTCTACAAGTTTGACCCATGGGAACTCCCAAgtatgcaacttcatcacaaaaccaccttttcttttcctcctttcatgcaaacccactttatatttttccatgactaattgcttaccttatgaacccattgaatttttggatccaatatttattttccttttggtgtttttgtgtgttttttttag

upper sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G15510.1 (Arabidopsis thaliana), 5'ss of exon 1
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgta--atttaatcacttacacccataccaatcataaattaagaatttattattac--agcttatatatactattatcatgcatgtatattatctaaa---aaa--------------------------------------------------------
|| || |||||||||||    || || ||||| | |||  | || ||| ||||||||||||| ||||||||||| || || ||||| ||||| || |||||||||||  |  | ||||    || |   | |||  |    || | | | || |||||      ||||||  | |  |  | |   | |   ||||    |   |||                                                        
GTTGTTCACTACCTCAAACGCAAAGCAGCCTCTGCTCCTTTACCTGTCGCCATCATCGCCGAAGTCGATCTCTATAAATTTGATCCATGGGAACTTCCCGgtacgtacgacctcatcatcatcatcatcaacaactacttttttata-tatagtattatttgatttatatgaatttgtgaccttttttttggttatgatgatctaaatctttttcttcttttttctataatttttttttggtttgtggattcgtttgttgcag

upper sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv19s0014g03300.t01 (Vitis vinifera), 5'ss of exon 1
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatcacttacacccataccaatcataaattaagaatttat-tattacagcttatatatacta--ttatcatgcatgta----tattatctaaaaaa-------
|| || ||||| || |||||||||||| | || | ||| || || ||| |||| ||||| ||||| |||||||| ||||| ||||||||||| ||||||||||  | |  | |  ||     |  ||    || | | |||| |   |||| ||| |    || ||| ||  |  |||  | | | |      |  ||| | |  ||       
GTAGTTCACTATCTGAAGAAGAAGGCCTCATCTGCTCCTCTTCCGGTCGCCATAATCGCAGAGGTTGATCTCTATAAGTTTGATCCCTGGGAACTCCCCGgtaacttacatcaa-accccagctaattatgatta-agattatgtgattatgtatgatgaattgtatgtaaaaggttagaaagaaagccatgctgatatttgatcaattctcag

upper sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S15_200V6.1 (Physcomitrella patens), 5'ss of exon 1
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatc--acttacacccatacca-atcataaattaagaatttattattacagcttatatatactattatcat-gcatgtatattatctaaaaaa
||| |||||||||||     |||||||| ||| |   |  ||    || || |||| ||||||||| | |||||||||||||| || |||||||||||  ||| |   ||   ||  ||| |  |  | || | ||||  ||  ||    | ||  ||     | |||  | ||      || | ||   || | || ||    
GTGCTGCACTACCTCCGTCGGAAGGCCGACTCTGACGCCTTCAAAATCCCCGTCATAGCCGAGGTCAACCTCTACAAGTTCGACCCTTGGGATCTCCCTAgtaagcttttctctctgactgattcgaaaacaacatcaccaa--aatgggtgatgtttctcaataataggtgcttgagaaatcgaatacttaatgtccaacc--

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|7274048|gb|C99336.2|C99336
EST:     CATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCG                         AGAAGGCGAACTTCGGGGAGCAGGAGTGGTATTTCTTCAGCCCGAGGGACC
genomic: CATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatt ... tttgtatcagAGAAGGCGAACTTCGGGGAGCAGGAGTGGTATTTCTTCAGCCCGAGGGACC




















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: 52 (upstream exon), 24 (downstream exon)
Score: 1

GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatt ... tttgtatcagAGAAGGCGAACTTCGGGGAGCAGGAGTGGTATTTCTTCAGCCCGAGGGACCGCAAGTACCCGAACGGGGCGCGGCCGAACCGGGCGGCGACGTCGGGGTA




<











<


<