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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGCTCCATTGTTTTTGTACTTCATCCAATGGCTGGACTGCGGCTGCTGTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgcagtatgtggttctgaaatttggacctcttatatatattttttctgtacaggagacctgggtttcatgcattaaaatctgttatgttttgttttcgcag

Basic information

species Zea mays
transcript GRMZM2G171967_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171967_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g17400.2 (Oryza sativa), 5'ss of exon 2
CCTGGCTCCATTGTTTTTGTACTTCATCCAATGGCTGGACTGCGGCTGCTGTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgcagtatgtggttctgaaatttggacctcttatatatattttttctgtacaggagacctgggtttcatgcattaaaatctgttatgttttgttttcgcag
 ||||| ||||| ||| | ||| ||||||| |||||||| || |||||||||||||| |||||||| ||| ||||  | |||||||||||||| |||||||||  | || ||||||    | || |  || |  |    |  |||  ||  | || |     |  || |  |||| ||  | |  | |||    |   | | ||    
ACTGGCGCCATTCTTTCTTTACCTCATCCAGTGGCTGGATTGTGGCTGCTGTTATGCTCTTCCCAGTTATCTAGGCCTTTTTCACATTCTCATTTGCAAGgtaccactgaagtatggatgtatgtatctttgtacaagaaagtatggttgct-tgcatttatgggcttg--ttca-gctgtcatttttgtggc-tgcagctgtca---
















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|211383694|gb|FL114695.1|FL114695
EST:     GTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAG                         GTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGC
genomic: GTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgc ... gttttcgcagGTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGC
EST: gi|211383689|gb|FL114690.1|FL114690
EST:     GTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAG                         GTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGC
genomic: GTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgc ... gttttcgcagGTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGC
EST: gi|211383693|gb|FL114694.1|FL114694
EST:     GTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAG                         GTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGC
genomic: GTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgc ... gttttcgcagGTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGC
EST: gi|78076532|gb|DV504966.1|DV504966
EST:     GTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAG                         GTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGC
genomic: GTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgc ... gttttcgcagGTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGC
EST: gi|211383690|gb|FL114691.1|FL114691
EST:     TTATGCCCTTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCTAG                         GTTTATGCTGATGGAGATAGCTCAGTGTCGA
genomic: TTATGCCCTT-CCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgc ... gttttcgcagGTTTATGCTGATGGAGATAGCTCAGTGTCGA
EST: gi|211383691|gb|FL114692.1|FL114692
EST:     GTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAG                         GTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGC
genomic: GTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgc ... gttttcgcagGTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGC

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), 45 (downstream exon)
Score: 28

CCTGGCTCCATTGTTTTTGTACTTCATCCAATGGCTGGACTGCGGCTGCTGTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgc ... gttttcgcagGTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGCCTTAGGGAATTCTACG


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 19

CCTGGCTCCATTGTTTTTGTACTTCATCCAATGGCTGGACTGCGGCTGCTGTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgc ... gttttcgcagGTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGCCTTAGGGAATTCTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 27

CCTGGCTCCATTGTTTTTGTACTTCATCCAATGGCTGGACTGCGGCTGCTGTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgc ... gttttcgcagGTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGCCTTAGGGAATTCTACG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 53

CCTGGCTCCATTGTTTTTGTACTTCATCCAATGGCTGGACTGCGGCTGCTGTTATGCCCTTCCCAGCTATTTAGGATTGTTTCACATTCTCATATGCAAGgtaaaattgc ... gttttcgcagGTTTATGCTGATGGAGATAGCTCAGTGTCGACATATGAAAGGCGGGCAAGCCTTAGGGAATTCTACG