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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttcacttttttgctaccttgaagctacctggatcacttgaccttcatgctgaatccggcttaccatgcccctgcag

Basic information

species Zea mays
transcript GRMZM5G876003_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876003_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g38060.2 (Oryza sativa), 5'ss of exon 7
GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttcacttttttgctaccttgaagctacctgg--atcacttgaccttcatgctgaatccggcttaccatgcccctgcag------------------------------------
|||| |||||||| |||||||||||||||| | ||| |||||||||| ||||   |   |    |||||| |    || ||   || |||  |   |             | |||   | |  ||  ||                                    
GATGCGAAAAACAAAATGTTCATTCTGTTCCATTTCCGGAAAAAGgtcagttatgccactgccgtaccttaattgcacttgaaaattactctatactttgatcattgagagattattgttcagctatagtctggcattgaatgctgtggtttcacgtctttgcag
















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|60395258|gb|DN228127.1|DN228127
EST:     GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN                         NNNNNNNGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
genomic: GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
EST: gi|78093364|gb|DV521738.1|DV521738
EST:     GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN                         NNNNNNNGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
genomic: GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
EST: gi|78074349|gb|DV502783.1|DV502783
EST:     GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN                         NNNNNNNGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
genomic: GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
EST: gi|148948105|gb|EC893614.2|EC893614
EST:     GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN                         NNNNNNNGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
genomic: GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
EST: gi|74240434|gb|DT648348.1|DT648348
EST:     GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN                         NNNNNNNGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
genomic: GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
EST: gi|74235314|gb|DT643228.1|DT643228
EST:     GATGTGAAAAACAGAATGTTCATTCTGTTTTACTTCAGGNNNNNN                         NNNNNNNGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
genomic: GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
EST: gi|78093365|gb|DV521739.1|DV521739
EST:     GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN                         NNNNNNNGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
genomic: GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
EST: gi|76923219|gb|DV169381.1|DV169381
EST:     GATGTGAAAAACAGAATGTTCATTCTGTTTTACTTCAGGNNNNNN                         NNNNNNNGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC
genomic: GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGC

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: 43 (upstream exon), 47 (downstream exon)
Score: 28

GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGCTTGTACAAACGGCGATGAGCCGCTTGTCTCGTATCCACCAGTAATACTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 45

GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGCTTGTACAAACGGCGATGAGCCGCTTGTCTCGTATCCACCAGTAATACTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 35

GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGCTTGTACAAACGGCGATGAGCCGCTTGTCTCGTATCCACCAGTAATACTG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 48

GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAGgttagtttca ... gcccctgcagGAAAAAAGTAAGGTGGCGAAGAGCATCGATTGGCCACAGCTGAAACCGTGCTTGTACAAACGGCGATGAGCCGCTTGTCTCGTATCCACCAGTAATACTG