Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcttgatataccctcactttgtgtatcttgcttgcttgctgtcgtatcatcatcatcatcatcatctcctgcttggttcagTTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGGCTTCGCTGGTCCCTATAGTTGGCGGAATACTCCTGACTTCGGTGACAGA

Basic information

species Zea mays
transcript GRMZM2G127591_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127591_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g59550.1 (Oryza sativa), 3'ss of exon 3
--------------------------------gtatatcttgatataccctcactttgtgtatcttgcttgcttgctgtcgtat-catcatcatc----atcatcatctcctgct-----tggttcagTTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGGCTTCGCTGGTCCCTATAGTTGGCGGAATACTCCTGACTTCGGTGACAGA
                                 |||  | | ||  |   ||  ||| |     ||      |||||   | ||  | || | ||    ||  ||  || |   |     |  | ||||||||||||||||| |||| |||||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||  | |||||
gtagagtcattttgcacctccttacatcatcactattccat-attcattttcgttttcttagcattatcatattgctacagcatgtaacaccctccctgatggtctgcttccaatccatgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGGCTTCGCTGGTCCCAATAGTTGGGGGAATACTCCTAACTTCAATAACAGA
















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|21843199|gb|BQ703780.1|BQ703780
EST:     CCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAG                         TTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAGgtatatcttg ... cttggttcagTTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGG
EST: gi|22520681|gb|BU079492.1|BU079492
EST:     CCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAG                         TTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAGgtatatcttg ... cttggttcagTTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGG
EST: gi|148942798|gb|EC887827.2|EC887827
EST:     CCAGTCTCCCTTCATGCAGACAATCAAATCTTTCACTCCTGCCACCACAG                         TTATTCTGCAGTGGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGG
genomic: C-AGTCTCC-TTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAGgtatatcttg ... cttggttcagTTATTCTGCAGTGG-CTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGG
EST: gi|32827243|gb|CD966921.1|CD966921
EST:     CCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAG                         TTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAGgtatatcttg ... cttggttcagTTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGG
EST: gi|13149872|gb|BG320194.1|BG320194
EST:     CCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAG                         TTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATAT-GG
genomic: CCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAGgtatatcttg ... cttggttcagTTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGG

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: 151

TTCGTCTTCTGCATAAACATTGTGCTGGGAAATGTCAGCTTGCGCTACATCCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAGgtatatcttg ... cttggttcagTTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGGCTTCGCTGGTCCCTATAGTTGGCGGAATACTCCTGACTTCGGTGACAGA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 106

TTCGTCTTCTGCATAAACATTGTGCTGGGAAATGTCAGCTTGCGCTACATCCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAGgtatatcttg ... cttggttcagTTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGGCTTCGCTGGTCCCTATAGTTGGCGGAATACTCCTGACTTCGGTGACAGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 105

TTCGTCTTCTGCATAAACATTGTGCTGGGAAATGTCAGCTTGCGCTACATCCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAGgtatatcttg ... cttggttcagTTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGGCTTCGCTGGTCCCTATAGTTGGCGGAATACTCCTGACTTCGGTGACAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 59

TTCGTCTTCTGCATAAACATTGTGCTGGGAAATGTCAGCTTGCGCTACATCCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAGgtatatcttg ... cttggttcagTTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGGCTTCGCTGGTCCCTATAGTTGGCGGAATACTCCTGACTTCGGTGACAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcttgcttgctgtcgtatcatcatcatcatcatcatctcctgcttggttcagTTATTCTGCAGTGGCTAGTCTGGAGCAAGCATTTCGAGTGGCGCATATGGGCTTCGCTGGTCCCTATAGTTGGCGGAATACTCCTGACTTCGGTGACAGA
                                      tctcctgctt  CT-rich tract