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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgactcacaagattgcgtagtattttgtagagaagttctcttttgttatttcttaggtataagtgttgaggattgaattagatgtaaaactagacagtcctctattctgcatcttccaggtgccatttatcgtttatgacttctatacacctcttgcagGTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCAGTTGTTGTGACTCTTAA

Basic information

species Zea mays
transcript GRMZM2G169089_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169089_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g36800.1 (Oryza sativa), 3'ss of exon 4
gtaagtttgactcacaagattgcgtagtattttgtagagaagttctcttttgtt-----atttcttaggtat--aagtgttgaggattgaattagatgtaaaactagacagtcctctattctgcatcttccaggtgcca-tttatcgtttatgacttctatacacctcttgcagGTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCAGTTGTTGTGACTCTTAA
|||||||||  | ||    ||  |||||  ||| ||      || ||||||  |       | |||   |||  | || | | | ||  || |  |||  |||  | |  | |   |  | | | | || || |||||| |  |  ||| |||| ||   ||||||||||||||||||||||||| ||||||||| ||||||||||||||| | ||||||||||||||||||||| ||| ||
gtaagtttgttttactttgtta-gtagttctttatatttttattgtcttttcattcaaggctccttcactattgatgtatcgtgtatgtaagttcatgccaaaaga-attgcctgttgatttac-tgtttcaagtgccagtagacagttcatgattttggtacacctcttgcagGTGGTTATTCTTCTCCATATCGTTATTACAACATCTGTCCTTGTCTATCCAGTTGTTGTGATTCTAAA
















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|71768082|gb|DR966019.1|DR966019
EST:     TTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACAT                         GTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCA
genomic: TTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACATgtaagtttga ... cctcttgcagGTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCA
EST: gi|89248515|gb|DY620301.1|DY620301
EST:     TGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCCAT-GGTGAACAT                         GTGGGTATTCTACTCCATATCATTATAACAACATCTGCCATTGTCTATCCA
genomic: TGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTC-ATTGGTGAACATgtaagtttga ... cctcttgcagGTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCA
EST: gi|101391387|gb|EB817628.1|EB817628
EST:     TTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACAT                         GTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCA
genomic: TTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACATgtaagtttga ... cctcttgcagGTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCA
EST: gi|93015559|gb|EB641079.1|EB641079
EST:     TTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACAT                         GTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCA
genomic: TTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACATgtaagtttga ... cctcttgcagGTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCA
EST: gi|149037287|gb|EE155331.2|EE155331
EST:     TTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACAT                         GTGGTTATTCTACTCCATATCATTTATTACAACATCTGCCATTGTCTATCC
genomic: TTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACATgtaagtttga ... cctcttgcagGTGGTTATTCTACTCCATATCATT-ATTACAACATCTGCCATTGTCTATCC

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: 23

CCTCACTCTACCAGTTTTCCCACTAGTTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACATgtaagtttga ... cctcttgcagGTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCAGTTGTTGTGACTCTTAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 11

CCTCACTCTACCAGTTTTCCCACTAGTTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACATgtaagtttga ... cctcttgcagGTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCAGTTGTTGTGACTCTTAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 29

CCTCACTCTACCAGTTTTCCCACTAGTTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACATgtaagtttga ... cctcttgcagGTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCAGTTGTTGTGACTCTTAA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 22

CCTCACTCTACCAGTTTTCCCACTAGTTGCACTCATGGCTGAGAAGCTGATCACAAGAAAGCTCATTGGTGAACATgtaagtttga ... cctcttgcagGTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCAGTTGTTGTGACTCTTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgcatcttccaggtgccatttatcgtttatgacttctatacacctcttgcagGTGGTTATTCTACTCCATATCATTATTACAACATCTGCCATTGTCTATCCAGTTGTTGTGACTCTTAA
                                           cacctctt  CT-rich tract
                    atttat  TA-rich tract