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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAGCCCACAGAAAGTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaacatatgaattaatttctaagttcttccatagcccgtaatatctatgcatttttattttccatgacatgcttttttattgaactatcatgcag

Basic information

species Zea mays
transcript GRMZM2G077233_T05
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077233_T06 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g18630.1 (Oryza sativa), 5'ss of exon 8
ACAAGCCCACAGAAAGTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaacatatgaattaatttctaagttcttccatagcccgta-atatctatgcatttt---tattttccatgacatgcttttttattgaactatcatgcag
 |||||||   |||| ||||| |||||||||||||||||| |||||||||| | | ||||||||||| ||| ||||| ||  || |  || ||| | |   | ||     |  || |   | | ||||      |||||||||||  ||| |||   |||  |  ||| ||
GCAAGCCCCATGAAACTGTGCTCTCAGATTGGTCTCTGTGCATTTGATGGTACTCGTTCTGTCAGgtcagcacaacacatacatgacattttaattgccatcttaatatatctatgttcctcctttttgttccctttccatgacagacttgtttcacgaatgaatatgtag
















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|78179647|gb|DV550020.1|DV550020
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|12047192|gb|BF729331.1|BF729331
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|76291014|gb|DV030582.1|DV030582
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|60348336|gb|DN215309.1|DN215309
EST:     GTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|60396697|gb|DN229564.1|DN229564
EST:     ATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: ATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|8577168|gb|BE129805.1|BE129805
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|211384116|gb|FL248479.1|FL248479
EST:     CTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: CTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|60346328|gb|DN213301.1|DN213301
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|91876412|gb|EB406369.1|EB406369
EST:     TTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: TTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|83278626|gb|DV942634.1|DV942634
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATAGAATCTGTTG-TGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|6194440|gb|AW146544.1|AW146544
EST:     TGGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: TG-TGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
EST: gi|32858947|gb|CD998628.1|CD998628
EST:     GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAG                         CAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT
genomic: GTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTT

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), 47 (downstream exon)
Score: 479

ACAAGCCCACAGAAAGTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 401

ACAAGCCCACAGAAAGTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 852

ACAAGCCCACAGAAAGTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 649

ACAAGCCCACAGAAAGTGTGCACTCAGATTGGTCTCTGTGTATTTGATGGTGCCCATTCTGTCAGgttagctcaa ... tatcatgcagCAATCCAATTGAATCTGTTGTTGAGAAACAGAAGCGTGGTTCTGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGT