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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGCTGCATTTCCAACTCAATCAACAGCGCCAGCACCAGTATGGCTCTTCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAATCATCTCTCGCAgtaagactatttttactattcttttcagctttgttaggttgtgcctgcaagtccaaatatttgggagctacgtatttagtaacaaatgcagaatgcttgt...

Basic information

species Zea mays
transcript GRMZM2G036872_T02
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036872_T02 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os07g46450.2 (Oryza sativa), 5'ss of exon 13
CAGAGCTGCATTTCCAACTCAATCAACAGCGCCAGCACCAGTATGGCTCTTCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAATCATCTCTCGCAgtaaga--ctatttttactattctt----ttcagctttgttaggttgtgcctgcaagtccaaatatttgggagctacgtatttagtaacaaatgcagaatgcttgt
| ||||| ||| |||||||||| || ||||| || || |||||||||||||  | |||||||||||||| |  |||||| |||| ||| |||||| | ||||||||  | || |||   ||  ||    ||||  |   ||  |||    |||   ||||| |  |   | |  | | ||   | || ||| |   |  ||||   
CGGAGCTCCATCTCCAACTCAACCAGCAGCGTCAACATCAGTATGGCTCTTTGGCAGATGCAAATGATCGTTATCAACATCTTCCAAACCATCTCCCACAgtaagaaaccatatttttcatagttaacattcatttcaattttgtttgaactgtg-gtccagac-tccagaacatccata---aatatcaagtattggctgctac-
















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|18965228|gb|BM661464.1|BM661464
EST:     TCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAATCATCTCTCGCA                         GAACATTGTCCAAACGGGATTTGATAGGAGCGTTGCTTTCTGTAATCAAGA
genomic: TCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAATCATCTCTCGCAgtaagactat ... cttctaccagGAACATTGTCCAAACAGGATTTGATAGGAGCGTTGCTTTCTGTAATCAAGA
EST: gi|67039042|gb|CO465297.1|CO465297
EST:     TCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAACCATCTCTCGCA                         GAACATTGTCCAAACGGGATTTGATAGGAGCGTTGCTTTCTGGTAATTCAA
genomic: TCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAATCATCTCTCGCAgtaagactat ... cttctaccagGAACATTGTCCAAACAGGATTTGATAGGAGCGTTGCTTTCTG-TAAT-CAA
EST: gi|60337955|gb|DN204928.1|DN204928
EST:     TCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAATCATCTCTCGCA                         GAACATTGTCCAAACAGGATTTGATAGGAGCGTTGCTTTCTGTAATCAAGA
genomic: TCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAATCATCTCTCGCAgtaagactat ... cttctaccagGAACATTGTCCAAACAGGATTTGATAGGAGCGTTGCTTTCTGTAATCAAGA

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: 54

CAGAGCTGCATTTCCAACTCAATCAACAGCGCCAGCACCAGTATGGCTCTTCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAATCATCTCTCGCAgtaagactat ... cttctaccagGAACATTGTCCAAACAGGATTTGATAGGAGCGTTGCTTTCTGTAATCAAGAGAAGCAAAGAAATGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 100

CAGAGCTGCATTTCCAACTCAATCAACAGCGCCAGCACCAGTATGGCTCTTCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAATCATCTCTCGCAgtaagactat ... cttctaccagGAACATTGTCCAAACAGGATTTGATAGGAGCGTTGCTTTCTGTAATCAAGAGAAGCAAAGAAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

CAGAGCTGCATTTCCAACTCAATCAACAGCGCCAGCACCAGTATGGCTCTTCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAATCATCTCTCGCAgtaagactat ... cttctaccagGAACATTGTCCAAACAGGATTTGATAGGAGCGTTGCTTTCTGTAATCAAGAGAAGCAAAGAAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 46

CAGAGCTGCATTTCCAACTCAATCAACAGCGCCAGCACCAGTATGGCTCTTCCGTAGATGCAAATGATCATCCTCAACACCTTCTAAATCATCTCTCGCAgtaagactat ... cttctaccagGAACATTGTCCAAACAGGATTTGATAGGAGCGTTGCTTTCTGTAATCAAGAGAAGCAAAGAAATGAG