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'   
12  
 5'  3'   
13  
 5'  3'   
14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggattattgtatgtgctcttactatgtatatcaggagcatactgttttatccattttctttgtctgtctttagGTGAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTTGTTGAGTTTGACTCTGTTGAAACTGCTACCGGTGTGTGCAAGGATCTAC

Basic information

species Zea mays
transcript GRMZM2G031529_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031529_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g52200.1 (Oryza sativa), 3'ss of exon 11
gtatggat-tattg--tatgtgctcttactatgtatatcaggagcatactgttttatccattttctttgtctgtctttagGTGAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTTGTTGAGTTTGACTCTGTTGAAACTGCTACCGGTGTGTGCAAGGATCTAC
|||||| | | || |||| || | | | | || || | | | | | ||| | | | ||| |||| |||||||| ||||||| |||||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||| ||| |||| |||||||||||||
gtatggttgcaatgcttatgggcattgaatggagttttccagatctcattctcaaacatctttgttggatatctctacagGTTAAGAAGCACATTAAGAATGGCAAGAATGTTTCGATGGGATTTGGCTTTGTTGAGTTCGACTCAGTTGAAACTGCAACCAGTGTCTGCAAGGATCTAC

upper sequence: GRMZM2G031529_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G09970.1 (Glycine max), 3'ss of exon 12
---------gtatggattattgtatgtgctcttactatgt---atatcaggagcatactgttttatccatttt--ctttgtctgtctt-----tagGTGAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTTGTTGAGTTTGACTCTGTTGAAACTGCTACCGGTGTGTGCAAGGATCTAC
||| | | | | | || | |||| | |||| | || || ||||| ||||| | | ||||||||||||||| | || || || || |||||||| ||||| ||||| ||||||||||||||||| |||||||||||| ||| ||||| ||| |||
gtattggttttatttctaactctttatgacttggctatatttcatatttttgttttgttgcttctcttattttggttttgttgctttcacaaatagGTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTTGTTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTAC

upper sequence: GRMZM2G031529_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA14G24510.1 (Glycine max), 3'ss of exon 9
------------------gtatggattattgtatgtgctcttactatgtatatcaggagcatactgttttatccattttctttgtctgtctt-tagGTGAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTTGTTGAGTTTGACTCTGTTGAAACTGCTACCGGTGTGTGCAAGGATCTAC
| | || || || ||| | | | | | || || | | || | || | | | ||||||||||||||| | || || || || |||||||| ||||| ||||| ||||||||||||||||| |||||||||||| ||| |||| ||| |||
gtattggtttagttgctaactcataatgacttagctgtatttcatatttttgttttgttgcttctcttatgttggttctgttgctttcacaagtagGTGAAGAAGCATCTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTTGTTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAGAGATTTAC

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|33095420|gb|CF055414.1|CF055414
EST:     GTACAAAGCTAAAGAGTGGCAGTCTTAAAAGTGCAACG                         GTTAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTT
genomic: GTACAAAGCTAAAGAGTGGCAGTCTTAAAAGTGCAACGgtatggatta ... ctgtctttagGTGAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTT




















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), 46 (downstream exon)
Score: 65

ATCTGTGTTTGTCAAGAACTTAAATTTCAAGACAACAGATGAATCATTGAAGCAGCATTTCAGTACAAAGCTAAAGAGTGGCAGTCTTAAAAGTGCAACGgtatggatta ... ctgtctttagGTGAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTTGTTGAGTTTGACTCTGTTGAAACTGCTACCGGTGTGTGCAAGGATCTAC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 43

ATCTGTGTTTGTCAAGAACTTAAATTTCAAGACAACAGATGAATCATTGAAGCAGCATTTCAGTACAAAGCTAAAGAGTGGCAGTCTTAAAAGTGCAACGgtatggatta ... ctgtctttagGTGAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTTGTTGAGTTTGACTCTGTTGAAACTGCTACCGGTGTGTGCAAGGATCTAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 32

ATCTGTGTTTGTCAAGAACTTAAATTTCAAGACAACAGATGAATCATTGAAGCAGCATTTCAGTACAAAGCTAAAGAGTGGCAGTCTTAAAAGTGCAACGgtatggatta ... ctgtctttagGTGAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTTGTTGAGTTTGACTCTGTTGAAACTGCTACCGGTGTGTGCAAGGATCTAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 32

ATCTGTGTTTGTCAAGAACTTAAATTTCAAGACAACAGATGAATCATTGAAGCAGCATTTCAGTACAAAGCTAAAGAGTGGCAGTCTTAAAAGTGCAACGgtatggatta ... ctgtctttagGTGAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTTGTTGAGTTTGACTCTGTTGAAACTGCTACCGGTGTGTGCAAGGATCTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactatgtatatcaggagcatactgttttatccattttctttgtctgtctttagGTGAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTTGTTGAGTTTGACTCTGTTGAAACTGCTACCGGTGTGTGCAAGGATCTAC
 ctcttac  putative branch site (score: 32)
 ttttatccattttctt  putative PPT
 attttcttt  TA-rich tract