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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgctgcactgaacttctttctccgtgtgtaaattatctggttctctcctaacatactgtctcaaatttgtgcag

Basic information

species Zea mays
transcript GRMZM2G044092_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044092_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g67220.3 (Oryza sativa), 5'ss of exon 10
-----------------------------------------------------------------AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgctgcactgaacttctttctc-----cgtgtgtaaattatctgg-ttctctcctaacatactgtctcaa-atttgtgcag
                                                                 |||||||||| | |||||||||||||||||||||||||||||     | ||     ||| ||||     |  ||||||||| | ||| || | ||||||||||   | |||| |||| |||||
GATATCTTCCATTTTTGCAAAACCTTATGATCAAACTATTTGTAACATTTGTTTACTTTTTGCAGAAAAATGGAACACTGGTGAAAAAATTGGTGAAAGGgtcagaactgatctctctctctctctctctctctctcgtgtaaattctgtggattatgtcctaacatatcatgtcaacatttttgcag

upper sequence: GRMZM2G044092_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g67220.2 (Oryza sativa), 5'ss of exon 10
AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgctgcactgaacttctttctccgt-----gtgtaaattatctgg-ttctctcctaacatactgtctcaa-atttgtgcag
|||||||||| | |||||||||||||||||||||||||||||     | ||     ||| ||||  |     ||||||||| | ||| || | ||||||||||   | |||| |||| |||||
AAAAATGGAACACTGGTGAAAAAATTGGTGAAAGGgtcagaactgatctctctctctctctctctctctctcgtgtaaattctgtggattatgtcctaacatatcatgtcaacatttttgcag
















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|76282020|gb|DV021588.1|DV021588
EST:     GAAAAAATT-GTGAAAGG                         GGTGCATTTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
genomic: GAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
EST: gi|149042712|gb|EE047227.2|EE047227
EST:     AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGG                         GCTGCTTCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
genomic: AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
EST: gi|32804368|gb|CD956604.1|CD956604
EST:     AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGG                         GCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
genomic: AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
EST: gi|71312816|gb|DR792938.1|DR792938
EST:     TAGAAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGG                         GCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
genomic: TAGAAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
EST: gi|6227160|gb|AW155689.1|AW155689
EST:     AAAAATGGAATAGTGGTGAAAAAATTGGAGAAAGG                         GCTGCATCTGAATGGCTTTTCATAGTTCCTTGTGGCCTTCATAAGTCACTT
genomic: AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
EST: gi|67011065|gb|CO439814.1|CO439814
EST:     AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGG                         GCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
genomic: AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
EST: gi|45568386|gb|CK986040.1|CK986040
EST:     AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGG                         GCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
genomic: AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
EST: gi|5296321|gb|AI783091.1|AI783091
EST:     AATAGTGGTGAAAAAATTGGTGAAAGG                         GCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
genomic: AATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
EST: gi|78022703|gb|DV491090.1|DV491090
EST:     AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGG                         GCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
genomic: AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
EST: gi|6056670|gb|AW091075.1|AW091075
EST:     AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGG                         GCTGCATCTGAATGTCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT
genomic: AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTT

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: 66

AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTTAATTATATAGCGAAGAAGTACAATAATCCAGCAATTTATGTTACTGAGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 86

AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTTAATTATATAGCGAAGAAGTACAATAATCCAGCAATTTATGTTACTGAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTTAATTATATAGCGAAGAAGTACAATAATCCAGCAATTTATGTTACTGAGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 43

AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgc ... atttgtgcagGCTGCATCTGAATGGCTTTTCATAGTTCCTTGGGGCCTTCATAAGTCACTTAATTATATAGCGAAGAAGTACAATAATCCAGCAATTTATGTTACTGAGA