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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCCCAAGGAGCCCTACGTCGGCAAGTGCCTCCTCAACACCAAGATCACCGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaactcatcatccatcctatccaatccaatccaatccaatccaatccttgattactcactactcaggattgcag

Basic information

species Oryza sativa
transcript LOC_Os06g01850.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G168143_T01 (Zea mays), 5'ss of exon 1
AGGCCCAAGGAGCCCTACGTCGGCAAGTGCCTCCTCAACACCAAGATCACCGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgt-----ctgtaactcatcatccatcctatccaatccaatccaatccaatc---caatccttgattactcac--tactcaggattgcag---------------------------
| |||||||||||| |||||||||| |||||||||||||||||||||||||| |||||||||||| || ||||| ||||||||||||||||||||||| |||     |||    |||  |   |  ||      | |   |   | |  ||   |||    ||  | |  |   ||   |  |  || |                           
AAGCCCAAGGAGCCGTACGTCGGCAGGTGCCTCCTCAACACCAAGATCACCGGCGACGACGCGCCGGGGGAGACGTGGCACATGGTCTTCAGCACCGAAGgtaggtactgaggttcaaaaaaaaatctgatttttgctgcctcgttcgttcgttcaactgctgtattcgtatcgtatgtataaacgctgatggacgcacgtatgcaccgcacgcag

upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA16G23710.1 (Glycine max), 5'ss of exon 2
AGGCCCAAGGAGCCCTACGTCGGCAAGTGCCTCCTCAACACCAAGATCACCGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaactcat-catccatcctatccaatccaatccaatcca--atccaatccttgattactcactactcaggattgcag--------------------------------------------
|  ||||||   || ||||| || |  ||||| |||||||| |||||||| |  || || || || || || || |||||||||||||||||||||||||||  |   ||||| | |    ||| |    |||  |||  ||    |    | ||   ||    |   |   || ||||| |                                            
AAACCCAAGACCCCTTACGTTGGTAGATGCCTGCTCAACACAAAGATCACTGGGGATGATGCTCCAGGAGAAACTTGGCACATGGTCTTCAGCACCGAGGgttggatgctcattcgttttccctctattttcctttcctttcttttactttaccccccatagagcgtaaagtag-attgctgataaaatttgtgtttttgagctaaaattagtgttattattgcag

upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G05350.1 (Glycine max), 5'ss of exon 2
AGGCCCAAGGAGCCCTACGTCGGCAAGTGCCTCCTCAACACCAAGATCACCGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaactcat-catccatcctatccaatccaatccaatccaatccaatccttgat-tactcactactcaggattgcag--------------------------------------------------
|  ||||||   || ||| | || |  ||||| |||||||| |||||||| |  || || || || || || || |||||||||||||||||||||||||||| |   ||||| | |    ||| |    |||  |         |  | |     ||   |||  ||  | | |  | ||                                                  
AAACCCAAGACCCCTTACATTGGTAGATGCCTGCTCAACACAAAGATCACTGGGGATGATGCTCCAGGAGAAACTTGGCACATGGTCTTCAGCACCGAGGgtcggatgctcattcgttttccctctattttcctttttttgttcttttattttcctataccctccatagactgtaaagtagattgctgataaaatttgtgtttttgagcaaatttagtgttattattgcag

upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 5'ss of exon 2
AGGCCCAAGGAGCCCTACGTCGGCAAGTGCCTCCTCAACACCAAGATCACCGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaactcatcatccatcctatccaatccaatccaatccaatccaatccttgattactca--ctactcaggattgcag--------------
|  || ||| | || |||   ||    |||||  | ||||||||||||||||  || ||||| ||||| ||||| |||||||| ||||||| |||||| |||   |  || |         || |  | |  | |    |   |  || |  | ||          |  | ||| | |  |              
AAACCTAAGAACCCTTACACTGGTCGCTGCCTTTTGAACACCAAGATCACCGGTGATGACGCTCCCGGTGAGACTTGGCACATTGTCTTCACCACCGAAGgtaaatcccttaattagggggcttttgattgtatttt--ttagaggcatttttcgagggagagatttgattaggttggttgatgacttaggtgag

upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT5G66190.1 (Arabidopsis thaliana), 5'ss of exon 2
AGGCCCAAGGAGCCCTACGTCGGCAAGTGCCTCCTCAACACCAAGATCACCGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaactcatcatccatcctatccaatccaatccaatccaatccaatccttgattactca--ctactcaggattgcag---------
|  || ||| | || |||   ||    |||||  | ||||||||||||||||  || ||||| ||||| ||||| |||||||| ||||||| |||||| |||   |  || |         || |  | |  | |    |   |  || |  | ||          |  | ||| | |  |         
AAACCTAAGAACCCTTACACTGGTCGCTGCCTTTTGAACACCAAGATCACCGGTGATGACGCTCCCGGTGAGACTTGGCACATTGTCTTCACCACCGAAGgtaaatcccttaattagggggcttttgattgtatttt--ttagaggcatttttcgagggagagatttgattaggttggttgatgacttag

upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv18s0001g14450.t01 (Vitis vinifera), 5'ss of exon 2
AGGCCCAAGGAGCCCTACGTCGGCAAGTGCCTCCTCAACACCAAGATCACCGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaactc-atcatccatcctatccaatccaatccaa-----tccaatccaatccttgattactcactactcagga-ttgcag----------------------------------------------------------
|| |||||| | || ||| |||| || || ||||||||||||||||| || |  ||||| || || || ||||| ||||||||||| |||| ||| ||||||| |   ||  | ||| | |      |     |||  ||     ||   |    |  ||  ||  | | |  | || | |||                                                             
AGACCCAAGAATCCTTACATCGGAAAATGTCTCCTCAACACCAAGATTACTGGAGACGATGCTCCAGGAGAGACCTGGCACATGGTATTCACCACTGAGGgtcagcttctttaccatgcctatctctcttgataattgaaggatttcttttttcttttttcttttataattttttagtagttgtgaataaattatgggattattcttgcatttgattgttgcgttggataatctgataaaacag

upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv04s0023g03510.t01 (Vitis vinifera), 5'ss of exon 2
AGGCCCAAGGAGCCCTACGTCGGCAAGTGCCTCCTCAACACCAAGATCACCGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaactcatcatccatcctatccaatccaatcc--aatccaatccaatccttgattactcactactcaggattgcag----------------------------------------------------------------
| ||| ||| | || ||| | ||||  || || |||||||| ||||||||||  || || || || || || ||||||||||||||||||||||||||||||     ||   | |      | ||  |     ||    ||| |||   || | |   | | |   |    |   ||  ||                                                                
AAGCCTAAGAATCCTTACATTGGCAGATGTCTTCTCAACACTAAGATCACCGGGGATGATGCTCCTGGAGAAACATGGCACATGGTCTTCAGCACCGAGGgta-acgaccttttacatgctccatgtatatatattggaaattcaacagaaccatctttaattttatgtggaacttttgagttttttagctgatcgctcctgatttcttttgagctgaatttgattggtcaattgggttgctcag

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|88404627|gb|CI581063.1|CI581063
EST:     CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGG                         GTGAGATCCC-TACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGG
genomic: CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGG
EST: gi|88671965|gb|CI726081.1|CI726081
EST:     CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGG                         GTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
genomic: CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
EST: gi|58695210|gb|CK083897.1|CK083897
EST:     CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGG                         GTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
genomic: CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
EST: gi|88671055|gb|CI725171.1|CI725171
EST:     CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGG                         GTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
genomic: CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
EST: gi|88668144|gb|CI722883.1|CI722883
EST:     CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGG                         GTGAGATCCCCTANAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
genomic: CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
EST: gi|88955314|gb|CI721886.1|CI721886
EST:     CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGG                         GTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
genomic: CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
EST: gi|88955313|gb|CI721885.1|CI721885
EST:     CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGG                         GTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
genomic: CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
EST: gi|33798466|gb|CF325091.1|CF325091
EST:     ATGGTCTTCAGCACCGAGG                         GTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
genomic: ATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
EST: gi|29685685|gb|CB681960.1|CB681960
EST:     CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGG                         GTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
genomic: CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
EST: gi|88665792|gb|CI715948.1|CI715948
EST:     CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCCCCGAGG                         GTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
genomic: CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
EST: gi|88670049|gb|CI724165.1|CI724165
EST:     CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGG                         GTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG
genomic: CGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCG

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: 75 (upstream exon), 74 (downstream exon)
Score: 185

AGGCCCAAGGAGCCCTACGTCGGCAAGTGCCTCCTCAACACCAAGATCACCGCCGACGACGCGCCCGGCGAGACATGGCACATGGTCTTCAGCACCGAGGgtctgtaact ... aggattgcagGTGAGATCCCCTACAGAGAGGGGCAGTCCATCGGCGTCATCGCCGACGGCGTCGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAG




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