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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgttgattgtattctatttggtaggattccactgctaaagttcttcgcgttttcttatcctcgtcaaccatgttttttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCACGGAAGCGCATGAACTCCAACCGGTCGTACCAGTATGACCCACTGAACA

Basic information

species Zea mays
transcript GRMZM5G833124_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 11
gtaagcgttgattg------tattctatttggtaggattccactgct-aaagttcttcgcgttttcttatcctcgtcaaccatgttttttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCACGGAAGCGCATGAACTCCAACCGGTCGTACCAGTATG---ACCCACTGAACA
|||||  |||||        ||     ||||| |       |||| | ||| || || || || | | |||||  ||||   ||||||   || |||||||||||| ||||| ||||| || ||||| |||||||||||| |||||||||||||||| ||||||||||| ||||| |||||  |||   |||||||||   
gtaagtattgataacaaggttaacaactttggcaatgccatactggtcaaatttgtttgcattatatcatcctaatcaaatgtgttttg-gtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCACGGAAGCGGATGAACTCCAATCGGTCATACCAAAATGCAAACCCACTGA---
















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|6031379|gb|AW076236.1|AW076236
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCAT                         GCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttg ... ttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
EST: gi|31363448|gb|CD447805.1|CD447805
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGACACTCTCAAAGCTGCTTTTCAT                         GCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttg ... ttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
EST: gi|91874041|gb|EB403998.1|EB403998
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCAT                         GCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttg ... ttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
EST: gi|84977310|gb|DW475732.1|DW475732
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCAT                         GCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttg ... ttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
EST: gi|32849185|gb|CD988866.1|CD988866
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCAT                         GCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttg ... ttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
EST: gi|93281684|gb|EB673948.1|EB673948
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCAT                         GCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttg ... ttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
EST: gi|76016960|gb|DT944130.1|DT944130
EST:     CAGATGACATTCTCAAAGCTGCTTTTCAT                         GCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA
genomic: CAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttg ... ttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCA

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), 49 (downstream exon)
Score: 156

TGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttg ... ttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCACGGAAGCGCATGAACTCCAACCGGTCGTACCAGTATGACCCACTGAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 446

TGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttg ... ttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCACGGAAGCGCATGAACTCCAACCGGTCGTACCAGTATGACCCACTGAACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 348

TGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttg ... ttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCACGGAAGCGCATGAACTCCAACCGGTCGTACCAGTATGACCCACTGAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 398

TGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttg ... ttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCACGGAAGCGCATGAACTCCAACCGGTCGTACCAGTATGACCCACTGAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctaaagttcttcgcgttttcttatcctcgtcaaccatgttttttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCACGGAAGCGCATGAACTCCAACCGGTCGTACCAGTATGACCCACTGAACA
 tgctaaa  putative branch site (score: 398)
                                         ttttttatt  putative PPT
                                      atgttttttattaaca  TA-rich tract