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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggatttttaacatgttaaaccttgtttactatgtgcttgtggtttgctggttgtatgtttagacatgtatgttctccatctgcataatcagccttt...

Basic information

species Oryza sativa
transcript LOC_Os01g15310.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G038606_T02 (Zea mays), 5'ss of exon 4
GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggatttttaacatgttaaaccttgtttactatgtgcttgtggtttgct-ggttgtatgtttagacatgtatgttctccatctgcataatcagccttt
|| ||||| |||||||||||||||||||| |||||||| || ||||||||||| ||||||||||| |||||||||||||||||||||| |    |  | | ||| |   | | | |  ||  | |||||| |||| | | | |     |   || | ||   ||    | |  | | | 
GACGGTGACAAGTTTTGGAGGATGCCAGAGTGTTACATTCGCGGGAACACCATTAAGTATCTTCGAGTTCCTGATGAGgtatggatttcttggttaatgagcctagcc-aatctctatttcagttttgcttggttatttatgtgcttctccctgatttcttccttgtcattatgacatg

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G038606_T03 (Zea mays), 5'ss of exon 3
----------------------GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggatttttaacatgttaaaccttgtttactatgtgcttgtggtttgct-ggttgtatgtttagacatgtatgttctccatctgcataatcagccttt
                      || ||||| |||||||||||||||||||| |||||||| || ||||||||||| ||||||||||| |||||||||||||||||||||| |    |  | | ||| |   | | | |  ||  | |||||| |||| | | | |     |   || | ||   ||    | |  | | | 
TTTATGATGGCTCGAATTGCAGGACGGTGACAAGTTTTGGAGGATGCCAGAGTGTTACATTCGCGGGAACACCATTAAGTATCTTCGAGTTCCTGATGAGgtatggatttcttggttaatgagcctagcc-aatctctatttcagttttgcttggttatttatgtgcttctccctgatttcttccttgtcattatgacatg

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G095114_T01 (Zea mays), 5'ss of exon 4
GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggatttttaacatgttaaaccttgtttactatgtgcttgtggtttgctggttgtatgtttagacatgtatgttctccatctgcataatcagccttt----
|||||||| |||||||||||||||||||| |||||||| |||||||||||||| ||||||||||| ||||||||||||||||| |||| |    |  | |   | | | ||  | |  ||  | ||||||   ||  ||||||  |   | |   || |  ||  ||  |   ||||     
GATGGTGACAAGTTTTGGAGGATGCCAGAGTGTTACATTCGTGGGAACACCATTAAGTATCTTCGAGTTCCTGATGAGgtatgaatttcttggttaatgagggtagct-acactctatttcagttttgct---tggttgtttatgcgcttctaggcttctactttatttttttccttgtcat

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA03G37170.2 (Glycine max), 5'ss of exon 4
GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggatttttaacatgttaaaccttgtttactatgtgcttgtggtttgctggttgtatgtttagacatgtatgttctccatctgcataatcagccttt--------
|| || ||||  |||||||||||||| ||||| ||||| || || || || |||||||| ||||| || ||||||||||| || ||| |     |||       || | || || | ||| |  |||  | |||  || || | ||  |||  ||          | |   ||||||         
GACGGAGATAGATTTTGGAGGATGCCTGAATGCTACATACGAGGCAATACAATCAAGTACCTTCGAGTACCTGATGAGgtgtgtattgt----gtgtggtgtgctggtgac-attttctttt--tttatttgtta-attttaaaactggtaaatttgttgagaagaaagggagccttgccacagta

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA19G39780.1 (Glycine max), 5'ss of exon 4
GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggatttttaacatgttaaaccttgtttactatgtgcttgtg-gtttgctggttgtatgtttagacatgtatgttctccatctgcataatcagccttt----
|| || ||||  |||||||||||||| ||||| || || || || || || |||||||| ||||| |||||||||||||| || ||| |     |||  |    |  | ||  | |  || |   |||| |  ||  |    | |  |  |  |||    |   |   |    |||       
GACGGAGATAGATTTTGGAGGATGCCTGAATGCTATATACGAGGCAATACAATCAAGTACCTTCGAGTTCCTGATGAGgtgtgtattgt----gtgtgcagtgctaatgacattttatttttttatttgttaatttaaaaacttg-taaatgggttgagaagaagggaaccttgccacggtag

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA02G17430.2 (Glycine max), 5'ss of exon 4
GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggatt-----tttaacatgttaaacctt-gtttactatgtgcttgtggtttgctggttgtatgtttagacatgtatgttctccatc-tgcat--aatcagccttt----------------------------
||||| ||||  |||||| | ||||| || || ||||| ||||| || ||||| ||||| |||||||||||||||||||| ||   |     || |  || ||     || | |   |  |||  |  ||||      || | |    |     ||| | ||||  |  |||||  | | | ||  |                            
GATGGAGATAGATTTTGGCGTATGCCTGAGTGCTACATTCGTGGCAATACCATTAAGTACCTTCGGGTTCCTGATGAGgtgtgtgctgctgcttcagtatttttgttttttgctctttcagtgaataaggttcagaacttct-tagggaatgtcgtaagctctcggtgatgcatgcatttatccactgatttaaatttacttcctgttcatttag

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G27720.1 (Arabidopsis thaliana), 5'ss of exon 5
GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggatttttaacatgttaaaccttgtttactatgtgcttg---tggtttgctggttgtatgtttagacatgta-tgttctccatctgcataatcagccttt
|| || ||||  |||||||||||||| |||||||| |||||||| ||||| |||||||| ||||| ||||| |||||||||    |||||    |||       | | ||     ||||||   | ||||  |  ||||     |     || | || |     |  ||  ||||||     
GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgta--atttttttttgtgtgtgtgtgtatatatctcttgcttgatctagttttttctttgttcccctctctctggaatgatgatgcttagccaaatcagata--

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv14s0060g02240.t01 (Vitis vinifera), 5'ss of exon 4
GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatg---gatttttaac--atgttaaaccttgtttactatgtgcttgtggtttgctggttgtatgtttagacatgtatgttctccatctgcataatcagccttt
||||| |||| ||||||||| ||||||||||| ||||| |||||||| || || ||||||||  | || ||||| |||||||    | ||||| |   || |  ||  ||     |||| |   | |  | | |   || |||| ||     | |||   ||  || |  | |  |    |  
GATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAGgtatatttggtttttcattgatatctaagtttaaa-gctatattgctattatattcatatt-tatgcttctttgt-tataggctatatttctaaaccccaagt--

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggatttttaacatgttaaac-cttgtttactatgtgcttgtggtttgctggttgtatgtttagacatgtatgttctccatctgcataatcagccttt-----
||||| |||| ||||||||| ||||| || || |||||||||||||| || || || |||||||| |||||||||||||||||    | | | || ||   | | ||||||   |     | ||   |    || | || | | |  | ||   ||    |  ||  |  |   ||| |     
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatg----tctgaaatcttcctcacatgtttaagctaaatctatgaccttacagt-gcat-tcttgttacgttctttgcttagttgtcttttggtcctattttgt

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ10085 (Selaginella moellendorffii), 5'ss of exon 3
GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatg-gatttttaa-catgttaaaccttgtttactatgtgcttgtggtttgctggttg--tatgtttagacatgtatgttctccatctgcataatcagccttt
||||| ||   ||||||||| ||||| || || |||||| | || |||||||||||||||||||| ||||| || |||||  | |||||  |  |  ||||   |     |  | ||||   | |   | ||   |   |  ||||  ||  |                             
GATGGAGACCGGTTTTGGAGAATGCCCGAGTGCTACATCAGGGGCAACACCATCAAGTATCTTCGTGTTCCAGACGAGgtgagcgatttccattcgcgttactgccgagcttgtttgtgagggagagatcctcactcacttcgtttgaaccag-----------------------------

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|88848532|gb|CI087054.1|CI087054
EST:     TTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: TTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|88214587|gb|CI214436.1|CI214436
EST:     CACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: CACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|86504317|gb|CI146950.1|CI146950
EST:     CTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: CTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|88202538|gb|CI200893.1|CI200893
EST:     TGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: TGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|88979842|gb|CI026148.1|CI026148
EST:     AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|89199230|gb|CI255496.1|CI255496
EST:     AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|88208022|gb|CI207871.1|CI207871
EST:     AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|88241907|gb|CI241756.1|CI241756
EST:     ACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: ACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|88214580|gb|CI214429.1|CI214429
EST:     AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|89170615|gb|CI039892.1|CI039892
EST:     AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|3761804|gb|C99052.1|C99052
EST:     AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|88241526|gb|CI241375.1|CI241375
EST:     TGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: TGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|87025899|gb|CI282476.1|CI282476
EST:     AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
EST: gi|89193834|gb|CI018152.1|CI018152
EST:     AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAG                         GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG
genomic: AATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG

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: 72 (upstream exon), 69 (downstream exon)
Score: 56

GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggattt ... tctatgacagGTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG




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