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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgcgcactgcccttggcgtgcgccctgctacgttactccgggacccgctgccggactaggttttgggtttcattatctgtttgtcttcgcgtcgattaggtggtgtgtggcgcgatctgacgcgggtttgtttgtttatcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA

Basic information

species Zea mays
transcript GRMZM2G171745_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 1
gttcgcgcactgcccttggcgtgcgccctgc-tacgttactccgggacccgctgccggactaggttttgggtttcattatctgtttgtcttcgcgtcgattaggtggtgtgtggcgcgatctgacgcgggtttgtttgtttatcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA
||    |     |||  | |   ||| | || | ||   | ||| |  |||| ||  |  |||| || ||||||        |     ||   | ||       || | |      |||||| | |   ||| |||        |  |||||||||||| |||||||| |||||||| |||||| ||||||| ||||||||||| || ||  |||| ||||||||||
gtataagggac-cccccgcctctcgctccgcctgcgccccgccgcg--ccgc-gcgtgtttagggttagggttttgggggtggaccacctctcc-tcccccctctgattt------cgatctaatgtcagttcgtt--------gatgcagCTCACTGGAACGCAGTATGCGTCGTCTCTGGACGTGCTCCGCCTCTTCGCCTATGGGACATTGAAGGACTACAAGA
















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|211178519|gb|FK980677.1|FK980677
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211180924|gb|FK980686.1|FK980686
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211178518|gb|FK980676.1|FK980676
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211178522|gb|FK980680.1|FK980680
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211180931|gb|FK980693.1|FK980693
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC

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: 171

TTCGTCCGCGCCCCAGCTCGCCGCGCTGGTGCTTGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

TTCGTCCGCGCCCCAGCTCGCCGCGCTGGTGCTTGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 125

TTCGTCCGCGCCCCAGCTCGCCGCGCTGGTGCTTGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

TTCGTCCGCGCCCCAGCTCGCCGCGCTGGTGCTTGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgattaggtggtgtgtggcgcgatctgacgcgggtttgtttgtttatcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA
                      atctgac  putative branch site (score: 138)
                                      tttgtttat  TA-rich tract