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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaattgcaatttctttggactggtctatagtattaccagttcatgttggtaggtgtgtcaaaggaatccactaacttagcatgtatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTG

Basic information

species Zea mays
transcript GRMZM2G003076_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 9
gtaagcaattgcaatttctttggactggtctatagtattaccagttcatgttggtaggtgtgtcaaaggaatccactaacttagcatgtatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTG
|||||    |  |||||||||||| |  |  | || |||   || |         |||      | || |||  ||||| ||      | | |||||| |||| |||||  |||||||||||| ||| || |||||||| ||||||||||| || ||||| ||| | |||||| ||
gtaagtgtgtagaatttctttggagtctttgaaagaatt--tagcttgctgaaacagg------agagaaat--actaagttgagccttgtcttgcagATGTGTCTCAACACATTTGATAAAGCAGCTGACCTTGATGTTCTGAACCATCCGATTCTGAATTTCTTTTATTACTTG
















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|18166177|gb|BM336016.1|BM336016
EST:     TGTGACTACCATCTGTTTTTCTTGTTTCTTGATCAGATGTGTCATG                         CTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCAT
genomic: TGTGACTACCATCTGTTTTTCTTGTTTCTTGATCAGATGTGTCATGgtaagcaatt ... tatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCAT
EST: gi|16920930|gb|BM074899.1|BM074899
EST:     TGTGACTACCATCTGTTTTTCTTGTTTCTTGATCAGATGTGTCATG                         CTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCAT
genomic: TGTGACTACCATCTGTTTTTCTTGTTTCTTGATCAGATGTGTCATGgtaagcaatt ... tatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCAT
EST: gi|148948893|gb|EC894307.2|EC894307
EST:     CTATGTGACTACCATCTGTTTTTCTTTGTT-CTTGATCAGATGTGTCATG                         CTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAAC
genomic: CTATGTGACTACCATCTGTTTTTCTT-GTTTCTTGATCAGATGTGTCATGgtaagcaatt ... tatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAAC
EST: gi|18163841|gb|BM333680.1|BM333680
EST:     CAGATGTGTCATG                         CTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCAT
genomic: CAGATGTGTCATGgtaagcaatt ... tatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCAT
EST: gi|71319323|gb|DR796414.1|DR796414
EST:     CTTGATCAGATGTGTCATG                         CTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCAT
genomic: CTTGATCAGATGTGTCATGgtaagcaatt ... tatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCAT

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), 48 (downstream exon)
Score: 44

GTTGGCTATGTGACTACCATCTGTTTTTCTTGTTTCTTGATCAGATGTGTCATGgtaagcaatt ... tatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 108

GTTGGCTATGTGACTACCATCTGTTTTTCTTGTTTCTTGATCAGATGTGTCATGgtaagcaatt ... tatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 106

GTTGGCTATGTGACTACCATCTGTTTTTCTTGTTTCTTGATCAGATGTGTCATGgtaagcaatt ... tatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 151

GTTGGCTATGTGACTACCATCTGTTTTTCTTGTTTCTTGATCAGATGTGTCATGgtaagcaatt ... tatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcatgttggtaggtgtgtcaaaggaatccactaacttagcatgtatattgcagCTGTGCCTCAATTCATTTGATAAAGAAGCAGATCTTGATGTCCTGAACCATCCAATCCTGAACTTCCTCTATTACCTG
                              cactaac  putative branch site (score: 151)
                                          atgtatatt  TA-rich tract