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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaattttgttttggtttgtttatatttcatctaaaaatttcaatttaaacttttttactccaacctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATAAAATTGAAACCTCCAACTCGAAGGATAATAAACTTGTACTCACAAGTGA

Basic information

species Zea mays
transcript GRMZM2G052403_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 18
gtaagtaattttgttttggtttgtttatatttcatctaaaaatttcaat---ttaaacttttttactccaacctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATAAAATTGAAACCTCCAACTCGAAGGATAATAAACTTGTACTCACAAGTGA---
|| || | |||  | |||  ||      |||| ||| |   | |||  |   ||||| | | || ||||||  ||||||||||||||||||||| ||||| || || || |||||||||||||||||||||||| | || | ||||||      ||||  |||||||||| |  | || ||   
gtgagcattttcttgttgtctta---gcattttatccatggaattctgtgtgttaaattgtgttgctccaaaatttcttagATGTGGACAAGATAGTTGGCTATGCTGTTAGTTATCACCTTAAGCACAATAAAGTCGAGATCTCCAA------GGATGGTAAACTTGTATTGGCGAGCGAAAG
















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|211048835|gb|FL187595.1|FL187595
EST:     CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA                         ATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA
genomic: CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAAgtaagtaatt ... cctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA
EST: gi|67034427|gb|CO462977.1|CO462977
EST:     CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA                         ATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA
genomic: CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAAgtaagtaatt ... cctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA
EST: gi|60399121|gb|DN231935.1|DN231935
EST:     CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA                         ATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA
genomic: CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAAgtaagtaatt ... cctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA
EST: gi|211051787|gb|FL187605.1|FL187605
EST:     CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA                         ATGTGGACAANATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA
genomic: CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAAgtaagtaatt ... cctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA
EST: gi|211051788|gb|FL187606.1|FL187606
EST:     CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA                         ATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA
genomic: CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAAgtaagtaatt ... cctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA
EST: gi|211048839|gb|FL187599.1|FL187599
EST:     CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAA                         ATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA
genomic: CAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAAgtaagtaatt ... cctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATA

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), 47 (downstream exon)
Score: 136

TTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAAgtaagtaatt ... cctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATAAAATTGAAACCTCCAACTCGAAGGATAATAAACTTGTACTCACAAGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

TTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAAgtaagtaatt ... cctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATAAAATTGAAACCTCCAACTCGAAGGATAATAAACTTGTACTCACAAGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

TTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAAgtaagtaatt ... cctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATAAAATTGAAACCTCCAACTCGAAGGATAATAAACTTGTACTCACAAGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

TTTCTGAGTCGCAATGGAATTGAATGCAATGATATTGAAGAATTATTCATCAAAGACCAATCACTGAGTAATGAAAgtaagtaatt ... cctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATAAAATTGAAACCTCCAACTCGAAGGATAATAAACTTGTACTCACAAGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatatttcatctaaaaatttcaatttaaacttttttactccaacctttcttagATGTGGACAAGATTGTTGGATACGCAGTGAGTTATCACCTTAAGCACAATAAAATTGAAACCTCCAACTCGAAGGATAATAAACTTGTACTCACAAGTGA
          atctaaa  putative branch site (score: 127)
                               cttttttactccaacc  putative PPT
     atttcatctaaaaatt  TA-rich tract