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

AACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatctacatttcaagtattttcttcaaggactaaatgtttactcacactgaaggtttggtaaatgtatttgcttctttcag

Basic information

species Zea mays
transcript GRMZM2G012501_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012501_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 15
AACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatcta--catt--------tcaagtattttcttcaaggactaaatgtttactcacactgaaggtt-----tggtaaatgtat-ttgcttctttcag
 |||||||||||  ||| ||||||||| ||||| ||     || |  |||| ||||||||||| ||| |||||||||||   ||||||||||||||| ||||||||| | |   |||        | || ||| |||||  |||   |  |||  ||||||||||||| ||     |  || |||||| ||| |||||  ||
GACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagcaaacaattaagtacaattaaatatgttcttggaggcacagctgtcaactcacactgaagattttttttcatatatgtatgttgattcttgtag
















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|31350725|gb|CD435082.1|CD435082
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
EST: gi|211320234|gb|FL338449.1|FL338449
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
EST: gi|74243906|gb|DT651820.1|DT651820
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGCGTTGAT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGAT
EST: gi|211280128|gb|FL354649.1|FL354649
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
EST: gi|211537215|gb|FL317072.1|FL317072
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
EST: gi|67021265|gb|CO450014.1|CO450014
EST:     TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGAT                         GTCACTGTTTGTGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT
genomic: TATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGT

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), 49 (downstream exon)
Score: 267

AACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGTTCAAAGCCTCTTGCAAGCTTGCCGTATAATTCACCTGGGCAAGTTTTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 289

AACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGTTCAAAGCCTCTTGCAAGCTTGCCGTATAATTCACCTGGGCAAGTTTTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 209

AACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGTTCAAAGCCTCTTGCAAGCTTGCCGTATAATTCACCTGGGCAAGTTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 341

AACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatct ... cttctttcagGTCACTGTTTGCGTTGATGCCTCAGATGCTGAGGAGTTTTCAGAGATTTGTTCAAAGCCTCTTGCAAGCTTGCCGTATAATTCACCTGGGCAAGTTTTTG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatctacatttcaagtattttcttcaaggactaaatgtttactcacactgaaggtttggtaaatgtatttgcttctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC