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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatag

Basic information

species Zea mays
transcript GRMZM2G044584_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044584_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g06474.1 (Oryza sativa), 5'ss of exon 2
AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattgttt----ttctagtttgagttgca-aggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatag--------
||||||||||||||  ||||||| |||| ||||||||||||| ||||||| ||||||||||| |||||||||||||| | |  ||    || |  ||  | || |  | |||| | ||||    ||      |  || | ||  ||||  | || ||   | ||         
AAAGCACTTGCAGGATTGAGAAGGATCAATTTAGATGGGTTGAGATGGCGTGTATTTGATGCAAAGGGTCAGgttagcaatccttctgattttgcttcaatttacggaagatgtatttatgtggaatgcaggaatggttatgcagtaagctactttgctgtttatgttgatag

upper sequence: GRMZM2G044584_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g15370.1 (Oryza sativa), 5'ss of exon 2
AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatag
||||||||||||||| |||||||||||| ||||||||| ||| ||||||| |||||||| || ||||| |||||||  ||| || | || |||  | | |  | | | |  ||  ||  ||| |  | ||       | |  | ||| | ||||  ||||
AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGTGTATTTGACGCAAAGGGCCAGgttaccattcttctgctggttccaatggttaagctaatgttcatgggaaatgttttga-----ccaagctactttgtttgtgcgatag

upper sequence: GRMZM2G044584_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g15360.6 (Oryza sativa), 5'ss of exon 1
----------------------------AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatag
                            |||||||||||||   |||||||||||| ||||||||| ||| ||||| | |||||||| || ||||| |||||||  ||| || |  | |||  |||||  | |   |  ||  ||   || || |      |   | |   || | | |||||||   
TGATAGTGCTGTTGTTTGAACTGAGCAAAAAGCACTTGCAGACTTGAGAAGAATCAATTTAGATGGTTTGAGATGGTGTGTATTTGACGCAAAGGGCCAGgttaccatttttctagtggttccagttgttaagcaaatattcatgggtaatggtttt---ttaccaagcctttgtttgtgtgatag--

upper sequence: GRMZM2G044584_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g15360.7 (Oryza sativa), 5'ss of exon 2
AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatag
                |||||||||||| ||||||||| ||| ||||| | |||||||| || ||||| |||||||  ||| || |  | |||  |||||  | |   |  ||  ||   || || |      |   | |   || | | |||||||   
-------------ACTTGAGAAGAATCAATTTAGATGGTTTGAGATGGTGTGTATTTGACGCAAAGGGCCAGgttaccatttttctagtggttccagttgttaagcaaatattcatgggtaatggtttt---ttaccaagcctttgtttgtgtgatag--

upper sequence: GRMZM2G044584_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g15360.2 (Oryza sativa), 5'ss of exon 2
AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatag
    |||||||||   |||||||||||| ||||||||| ||| ||||| | |||||||| || ||||| |||||||  ||| || |  | |||  |||||  | |   |  ||  ||   || || |      |   | |   || | | |||||||   
----CACTTGCAGACTTGAGAAGAATCAATTTAGATGGTTTGAGATGGTGTGTATTTGACGCAAAGGGCCAGgttaccatttttctagtggttccagttgttaagcaaatattcatgggtaatggtttt---ttaccaagcctttgtttgtgtgatag--

upper sequence: GRMZM2G044584_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv14s0171g00250.t01 (Vitis vinifera), 5'ss of exon 2
AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatag----------------
||||||||||| || |||||| |||||| ||| || || ||||||||||| ||||||||||| || || |||||| |||| |   || || | |||  |  || | | |   || | |  | |      |   | | | |    | ||||     | | |                
AAAGCACTTGCTGGCCTGAGACGAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgtt-ggatagaagtt-taatatga--taaaatggttattatagtttttagaaacccaataatataatgctggtctctactcccttttgggataagaaatgccag

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|211300790|gb|FL153837.1|FL153837
EST:     GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG                         GTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAG
genomic: GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAG
EST: gi|211203636|gb|FL470743.1|FL470743
EST:     GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG                         GTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAG
genomic: GAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 65

AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 108

AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattg ... tgtgatatagGTGCTCGGGCGATTGGCTTCCCAAATAGCTGTTGTGCTTCAAG