Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAAAATTTGGGATCCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagccattatctaaattacatattaaatactgcattgtcacttcgatcgtattgcagtgtctgtttttttatgatacatctgtctgatacttctgg...

Basic information

species Zea mays
transcript GRMZM2G074466_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074466_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g39380.2 (Oryza sativa), 5'ss of exon 24
GTAAAAATTTGGGATCCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagccattatctaaatta-catattaaatactgcat-tgtcacttcgatcgtattgcagtgtctgtttttttatgatacatctgtctgatacttctgg
|||||||| ||||||||||||||||||||||||||||||||  |||||||||||||||| ||||||||| |  ||| |||||| ||| |   || |||     ||     |   | |||||| | || ||| |  |    ||   || |||||  |    |      
GTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTTAAAGGGCACACTAGgtagaaatcatcatctaagttaaccagttcaatgaaatatgcactatcaccatcgtagttcactgtgttgtgaacta-actagatctgcttatctcagaca-

upper sequence: GRMZM2G074466_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G49040.1 (Arabidopsis thaliana), 5'ss of exon 24
GTAAAAATTTGGGATCCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagccattatctaaattacatattaaatactg-----cat-tgtcacttcgatcgtattgca---gtgtctgttttttta-tgatacatc-tgtctgatacttctgg---------------
|| |||||||||||||||||| |||||||||||||||||||||||||  | ||||| |||||| ||||    | |||   ||     | |  |   |   |      || | |   || | |  | || ||   |||   |||| ||||      | || | |||  |  |  |                 
GTTAAAATTTGGGATCCAAGTCTGCGTGGTTCTGAACTTCGAGCAACTTTGAAAGGACATACTGGgtatacactatttcttattcaccttgatggctctcgggagttatgtttttttttgttaatttttcatatgtggtggtttctttaacagcgcttcctttcttgttttcttttcaacttttgatgtag
















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|32841191|gb|CD980872.1|CD980872
EST:     CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAG                         GGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
genomic: CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
EST: gi|32840987|gb|CD980668.1|CD980668
EST:     CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAG                         GGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
genomic: CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
EST: gi|32841098|gb|CD980779.1|CD980779
EST:     CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAG                         GGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
genomic: CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
EST: gi|32840943|gb|CD980624.1|CD980624
EST:     CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAG                         GGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
genomic: CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
EST: gi|32840932|gb|CD980613.1|CD980613
EST:     CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAG                         GGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
genomic: CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
EST: gi|32841011|gb|CD980692.1|CD980692
EST:     CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAG                         GGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
genomic: CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
EST: gi|71437502|gb|DR818552.1|DR818552
EST:     CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAG                         GGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
genomic: CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
EST: gi|71437503|gb|DR818553.1|DR818553
EST:     CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAG                         GGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA
genomic: CCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 57

GTAAAAATTTGGGATCCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGATGATCAGTCTGTCATAGTATGGGATAAGCAGACTTTTAAGCTTTTGGAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 41

GTAAAAATTTGGGATCCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGATGATCAGTCTGTCATAGTATGGGATAAGCAGACTTTTAAGCTTTTGGAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 45

GTAAAAATTTGGGATCCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGATGATCAGTCTGTCATAGTATGGGATAAGCAGACTTTTAAGCTTTTGGAA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 19

GTAAAAATTTGGGATCCAAGTTTGCGTGGTTCTGAACTTCGAGCAACACTTAAAGGGCATACTAGgtagtagcca ... aaatttgcagGGCAATTCGAACAATCAGTTCAGATCGTGGCAAAATAGTTTCTGGAGCTGATGATCAGTCTGTCATAGTATGGGATAAGCAGACTTTTAAGCTTTTGGAA