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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatctttttgatttggtgaatcatagaagttgacaacatgtgcatgtctagctaattcatctaatttttttctttctacattaaactaaccgcatgc...

Basic information

species Zea mays
transcript GRMZM5G820727_T06
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G820727_T06 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g34750.1 (Oryza sativa), 5'ss of exon 3
GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatctttttgatttggtgaatcatagaagttgacaacatgtgcatgtctagctaattcatctaatttttttctttctacattaaactaaccg-catgc-
|||| |||||||| || || || || |||||||| || |||||  | |||||||||||||| ||||||||||||  |  |      ||| | || | || |  ||| |  | ||| ||   ||   || ||  |  |    |||| | | | || |  ||||     | ||  
GAAGCCAGTGCAATTCGGCTACACAAACATTTGACGGAGTTGACCTGATGGGTGAAAGGTTGGCAAATGAGgtacctaatgacttattgctcaaac-taaattttgtcctc-tgtacaaacctttgtagttgtttgatcgattttttgtgtgcacttgactatttatcttgtc

upper sequence: GRMZM5G820727_T06 (Zea mays), 5'ss of exon 3
lower sequence: AT4G25770.1 (Arabidopsis thaliana), 5'ss of exon 3
GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgta-tatctttttgatttggtgaatcatagaagttgacaacatgtgcatgtctagctaattcatctaatttttttctttctacattaaactaaccgcatgc
| ||  || | ||   ||| ||   |||||||||||||||||||  ||||||||||||| |||| ||||||||| ||| |   ||  ||| ||  || |          ||| ||         |  |||   || | |||| | | |||  | |||     |         
GTAGCGAGAGTAATAGTGCAACGTTGACATTTGATGGTGTTGATAAAATGGGTGAAAGGCTAGCTAATGAGgtagtatttggatgcattgttgtttcct------ctgtaacttgca-------acttaaa--atttgatttctatgtttgaaaatttgtgaag--------
















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|71772904|gb|DR970827.1|DR970827
EST:     CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAG                         GTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG
genomic: CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatcttt ... attattatagGTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG
EST: gi|78113514|gb|DV531905.1|DV531905
EST:     CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAG                         GTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG
genomic: CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatcttt ... attattatagGTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG
EST: gi|76020655|gb|DT947825.1|DT947825
EST:     CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAG                         GTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG
genomic: CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatcttt ... attattatagGTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG
EST: gi|78090975|gb|DV519349.1|DV519349
EST:     CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAG                         GTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG
genomic: CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatcttt ... attattatagGTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG
EST: gi|78082075|gb|DV510487.1|DV510487
EST:     CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAG                         GTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG
genomic: CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatcttt ... attattatagGTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG
EST: gi|78106692|gb|DV525110.1|DV525110
EST:     CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAG                         GTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG
genomic: CTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatcttt ... attattatagGTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTG

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), 45 (downstream exon)
Score: 25

GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatcttt ... attattatagGTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTGGCACATTCTCTTGGTGGCCTTGTTGCCAGATATGCTATAGGAAGGCTCT


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 22

GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatcttt ... attattatagGTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTGGCACATTCTCTTGGTGGCCTTGTTGCCAGATATGCTATAGGAAGGCTCT


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 18

GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatcttt ... attattatagGTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTGGCACATTCTCTTGGTGGCCTTGTTGCCAGATATGCTATAGGAAGGCTCT


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 25

GAAGTCAGTGCAACTCTGCCACTCAGACATTTGATGGTGTTGATTTAATGGGTGAAAGGTTAGCAAATGAGgtatatcttt ... attattatagGTTCTATCAGTTGTAGAGCAAAGACGAGGTGTGAAGAAAATCTCGTTTGTGGCACATTCTCTTGGTGGCCTTGTTGCCAGATATGCTATAGGAAGGCTCT