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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacaggctccccccagcatcgttagtgttatgataagtcctcgatagatttggcttcttgtgaatgctataatccaagttcgctcgttcttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACCTTTGAG

Basic information

species Zea mays
transcript GRMZM2G066362_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066362_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g07720.2 (Oryza sativa), 3'ss of exon 7
gtaagcacag----gctccccccag--catcgttagtgttatgataagtcctcgatag-----attt--------ggcttcttgtgaatgct-ataatccaagttcgctcgttcttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACCTTTGAG
|||||  |||    | || |  |||  | |  | |   | |  |||||| ||  | ||     ||||        |  ||  |||||||||| | ||| ||  |      ||||  || |||||||||||||||||  ||||||| || ||||||||||| ||||  |  |||  | ||||
gtaagttcagttgagttcacttcagttctttttcaccctcactataagttctaaagagcaggtatttctgttaatgttttgatgtgaatgctgaaaatgcacttctttctgttcacgtttgcagGTACTTCTATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAG
















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|211399029|gb|FL440152.1|FL440152
EST:     TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTG                         GTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
genomic: TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
EST: gi|76929770|gb|DV172154.1|DV172154
EST:     TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTG                         GTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
genomic: TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
EST: gi|71768738|gb|DR966675.1|DR966675
EST:     TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTG                         GTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
genomic: TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
EST: gi|50327839|gb|CO522965.1|CO522965
EST:     TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTG                         GTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
genomic: TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
EST: gi|211482896|gb|FL084116.1|FL084116
EST:     TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTG                         GTACTTCTATTCCTTGCCTTTKCTATTGTGGAAAACACGTTACCAGACACC
genomic: TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
EST: gi|101394908|gb|EB819388.1|EB819388
EST:     TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTG                         GTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTCCCAGACACC
genomic: TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
EST: gi|149069914|gb|EE158314.2|EE158314
EST:     TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTG                         GTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACCCC
genomic: TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
EST: gi|148950402|gb|EC895969.2|EC895969
EST:     TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTG                         GTACTTCTATTCCTTGCCTTTTTTATTGTGGAAAACACGTTACCAGACACC
genomic: TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
EST: gi|211289745|gb|FL473317.1|FL473317
EST:     TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTG                         GTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC
genomic: TTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACC

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), 48 (downstream exon)
Score: 82

ATATTGTAACTGTTATGTTTGTTGGCAACTTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACCTTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

ATATTGTAACTGTTATGTTTGTTGGCAACTTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACCTTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

ATATTGTAACTGTTATGTTTGTTGGCAACTTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACCTTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 64

ATATTGTAACTGTTATGTTTGTTGGCAACTTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTGgtaagcacag ... ttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACCTTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatttggcttcttgtgaatgctataatccaagttcgctcgttcttgtgtgcagGTACTTCTATTCCTTGCCTTTTCTATTGTGGAAAACACGTTACCAGACACCTTTGAG
                                      ctcgttctt  CT-rich tract
                       tataat  TA-rich tract