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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAGATGATGGATTCCCAACCATCACATTCCATTTTGAGGATGATCTTGCACTACATGTGTATCCCCATGAGTACTTTTTCGCAAATGGGgtaacatgacatttctctccaagtcgagtagtgtttaattcacccattgtcatgggttcatcacggtttcatcttatagcacttgaaagtggcttcagtg...

Basic information

species Zea mays
transcript AC190609.3_FGT004
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC190609.3_FGT004 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os04g26834.1 (Oryza sativa), 5'ss of exon 8
TGTAGATGATGGATTCCCAACCATCACATTCCATTTTGAGGATGATCTTGCACTACATGTGTATCCCCATGAGTACTTTTTCGCAAATGGGgtaacatgacatttctctccaagtcgagtagtgtttaattcacccattgtcatgggttcatcacggtttcatcttatagcacttgaaagtggcttcagtg---
 || |||||||  || ||||  ||||| |||||||||||| |||||||| |  |  |||||||||| || || ||||| |||| |||||||||||  | |||| || ||||| ||    | ||     |||      |  |       | |     ||| || |||||  ||| |  |||    |    ||   
AGTGGATGATGACTTTCCAAAGATCACTTTCCATTTTGAGAATGATCTTCCTTTGAATGTGTATCCACACGATTACTTCTTCGAAAATGGGgtaatgtaacatctcactcca-gtgatttggtcacctattggtatttctttgccaactta--gttgttacaacttatgacacctataaggttataacatgtta
















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|32870684|gb|CF010366.1|CF010366
EST:     TCGCAAATGGG                         AATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGAT
genomic: TCGCAAATGGGgtaacatgac ... ccttgagcagAATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGAT
EST: gi|37379778|gb|CF626648.1|CF626648
EST:     ATGATCTTGCACTACATGTGTATCCCCATGAGTACTTTTTCGCAAATGGG                         AATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGAT
genomic: ATGATCTTGCACTACATGTGTATCCCCATGAGTACTTTTTCGCAAATGGGgtaacatgac ... ccttgagcagAATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGAT
EST: gi|211431081|gb|FL481796.1|FL481796
EST:     ATGATCTTGCACTACATGTGTATCCCCATGAGTACTTTTTCGCAAATGGG                         AATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGAT
genomic: ATGATCTTGCACTACATGTGTATCCCCATGAGTACTTTTTCGCAAATGGGgtaacatgac ... ccttgagcagAATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGAT
EST: gi|86469808|gb|DY236178.1|DY236178
EST:     ATGATCTTGCACTACATGTGTATCCCCATGAGTACCTTTTCGCAAATGGG                         AATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGAT
genomic: ATGATCTTGCACTACATGTGTATCCCCATGAGTACTTTTTCGCAAATGGGgtaacatgac ... ccttgagcagAATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGAT

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: 45 (upstream exon), 46 (downstream exon)
Score: 44

TGTAGATGATGGATTCCCAACCATCACATTCCATTTTGAGGATGATCTTGCACTACATGTGTATCCCCATGAGTACTTTTTCGCAAATGGGgtaacatgac ... ccttgagcagAATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGATGGAAAGGACATTGTGCTTATGGGAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 51

TGTAGATGATGGATTCCCAACCATCACATTCCATTTTGAGGATGATCTTGCACTACATGTGTATCCCCATGAGTACTTTTTCGCAAATGGGgtaacatgac ... ccttgagcagAATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGATGGAAAGGACATTGTGCTTATGGGAG


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 39

TGTAGATGATGGATTCCCAACCATCACATTCCATTTTGAGGATGATCTTGCACTACATGTGTATCCCCATGAGTACTTTTTCGCAAATGGGgtaacatgac ... ccttgagcagAATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGATGGAAAGGACATTGTGCTTATGGGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 41

TGTAGATGATGGATTCCCAACCATCACATTCCATTTTGAGGATGATCTTGCACTACATGTGTATCCCCATGAGTACTTTTTCGCAAATGGGgtaacatgac ... ccttgagcagAATGACGTATACTGCGTGGGATTCCAAAATGGTGCATCACAGTCAAAGGATGGAAAGGACATTGTGCTTATGGGAG