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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttgaaacaatattttttctaacaacttttaagttattttgtttcataaaatattggcatgcatgcacagaattgacctgtttcattttgttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACACTGGAAACTCAATCATACTGTCTATTCCTTTGTAGCTGTCCAG

Basic information

species Zea mays
transcript GRMZM5G813909_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 9
gtatcttgaaacaatattttttctaacaacttttaagttattttgtttcataa-aatattggcatgcatgcacagaattgacctgtttcattttgttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACACTGGAAACTCAATCATACTGTCTATTCCTTTGTAGCTGTCCAG
                           |  |  |||||| ||| ||||||| | ||| |||   | ||||||   || | |||||  || |||||| | ||||||||||| | ||||||||| |||||||||||||| |||||||||||||| |||||||||||||| || ||||| |||||||||||||||||||||
------------------------gttatatgctaagttgtttagtttcattataattttgaattacatgcatgaaactcacctggatccttttgtcggtttcagTGTAGTAGTGAGGATGAAATAGTTTCTGTTATTGCACATGAACTTGGGCACTGGAAACTCAACCACACTGTGTATTCCTTTGTAGCTGTCCAG
















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|32909801|gb|CF014613.1|CF014613
EST:     NNNNNNNCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG                         TGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
genomic: GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
EST: gi|76293280|gb|DV032848.1|DV032848
EST:     GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG                         TGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
genomic: GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
EST: gi|71761327|gb|DR959264.1|DR959264
EST:     GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG                         TGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
genomic: GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
EST: gi|7162447|gb|AW520069.1|AW520069
EST:     GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG                         TGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGGCAC
genomic: GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
EST: gi|6194775|gb|AW146879.1|AW146879
EST:     GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG                         TGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
genomic: GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
EST: gi|78114997|gb|DV533385.1|DV533385
EST:     GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG                         TGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
genomic: GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
EST: gi|71758092|gb|DR956029.1|DR956029
EST:     GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG                         TGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
genomic: GTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
EST: gi|50322420|gb|CO517546.1|CO517546
EST:     ATTGATTCAGCAG                         TGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC
genomic: ATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 126

GCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACACTGGAAACTCAATCATACTGTCTATTCCTTTGTAGCTGTCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 88

GCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACACTGGAAACTCAATCATACTGTCTATTCCTTTGTAGCTGTCCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 121

GCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACACTGGAAACTCAATCATACTGTCTATTCCTTTGTAGCTGTCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 77

GCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaa ... ttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACACTGGAAACTCAATCATACTGTCTATTCCTTTGTAGCTGTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaaatattggcatgcatgcacagaattgacctgtttcattttgttgatttcagTGTAGCAATGAGGATGAGATAGTTTCTGTTATAGCACATGAACTTGGACACTGGAAACTCAATCATACTGTCTATTCCTTTGTAGCTGTCCAG
                                        ttttgtt  CT-rich tract
                                   tttcatttt  TA-rich tract