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

gtgagtttatcagctcttaattcatgtcatattggggttctattttttatttgcaatttttctaatgaatttattgcatttttcagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGACTGGCCAGCCTCTTGTACAATGCACTTCTCACATGTGCCCAATAAGAATC

Basic information

species Zea mays
transcript GRMZM2G071970_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 2
gtgagtttatcag-------ctcttaattcatgtcatattggggttctattttttatttgcaatttttctaatgaatttattgcattttt-cagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGACTGGCCAGCCTCTTGTACAATGCACTTCTCACATGTGCCCAATAAGAATC
||||||| || |        |||||| |||   || | ||| ||  | | ||||    |||||  || ||||  | ||   |||||||   ||| ||| |||||||| || ||||| | || |||||||| ||||| |||||||| || ||||||||||| ||||| ||||||||||||||||| || ||||||
gtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttc---tgcaaaattgctaacaagttccatgcatttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGACCGGTCAGCCTCTTGTCCAATGTACTTCTCACATGTGCCCGATCAGAATC
















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|32849583|gb|CD989264.1|CD989264
EST:     CCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         CGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGAC
genomic: CCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagtttat ... catttttcagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGAC
EST: gi|14190871|gb|BG833101.1|BG833101
EST:     CCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         CGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGAC
genomic: CCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagtttat ... catttttcagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGAC
EST: gi|31355260|gb|CD439617.1|CD439617
EST:     CCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         CGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGAC
genomic: CCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagtttat ... catttttcagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGAC
EST: gi|76932301|gb|DV172999.1|DV172999
EST:     CCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         CGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGAC
genomic: CCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagtttat ... catttttcagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGAC
EST: gi|14190870|gb|BG833100.1|BG833100
EST:     CCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAA                         CGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGAC
genomic: CCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagtttat ... catttttcagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGAC

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: 137

CCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagtttat ... catttttcagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGACTGGCCAGCCTCTTGTACAATGCACTTCTCACATGTGCCCAATAAGAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

CCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagtttat ... catttttcagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGACTGGCCAGCCTCTTGTACAATGCACTTCTCACATGTGCCCAATAAGAATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 117

CCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagtttat ... catttttcagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGACTGGCCAGCCTCTTGTACAATGCACTTCTCACATGTGCCCAATAAGAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 361

CCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCGACATGCTCATGTGGCTGCCAGAACCCAAGTGGGTCAAACTGTGTGAAgtgagtttat ... catttttcagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGACTGGCCAGCCTCTTGTACAATGCACTTCTCACATGTGCCCAATAAGAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggggttctattttttatttgcaatttttctaatgaatttattgcatttttcagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGACTGGCCAGCCTCTTGTACAATGCACTTCTCACATGTGCCCAATAAGAATC
                            ttctaat  putative branch site (score: 361)
                                             catttttc  putative PPT
      ttctattttttatttg  TA-rich tract