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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaacactgaccaaacaaactggcatacaaaatgctagcctggcatatctagactctttttatattacatgctaaaaccctgtcattttgcactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG

Basic information

species Zea mays
transcript GRMZM2G165535_T05
intron # 5
splice site 3'
intron type U2

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|78118501|gb|DV536885.1|DV536885
EST:     AATGGCCAACTAATTTGAAACCCAA                         AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
genomic: AATGGCCAACTAA-TTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
EST: gi|40334667|gb|CK368737.1|CK368737
EST:     CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA                         AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
genomic: CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
EST: gi|32919710|gb|CF024522.1|CF024522
EST:     CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA                         AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
genomic: CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
EST: gi|71771666|gb|DR969603.1|DR969603
EST:     CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA                         AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
genomic: CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
EST: gi|148950412|gb|EC895979.2|EC895979
EST:     CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA                         AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
genomic: CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
EST: gi|14646044|gb|BI180233.1|BI180233
EST:     CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA                         AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
genomic: CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
EST: gi|148943663|gb|EC888727.2|EC888727
EST:     CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA                         AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
genomic: CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
EST: gi|148947648|gb|EC893128.2|EC893128
EST:     AAATGGGCCAATTAA-TGGAACCCCAA                         AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
genomic: AAAT-GGCCAACTAATTGGAA-CCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
EST: gi|76280415|gb|DV019983.1|DV019983
EST:     CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAA                         AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
genomic: CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
EST: gi|32801826|gb|CD954062.1|CD954062
EST:     CCGAAAACGGCCTGGATGCACACAAAAATGGCCAACTAATTGGAACCCAA                         AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGGAATTTATTA
genomic: CCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGGAATTTATTA

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), 45 (downstream exon)
Score: 104

TTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

TTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 128

TTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

TTATTACTGATTATGATTACGTCTTCTCCGAAAACGGCCTGGTTGCACACAAAAATGGCCAACTAATTGGAACCCAAgtaagtctct ... cactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctagactctttttatattacatgctaaaaccctgtcattttgcactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG
                        tgctaaa  putative branch site (score: 138)
           tttttatattacatgc  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaacactgaccaaacaaactggcatacaaaatgctagcctggcatatctagactctttttatattacatgctaaaaccctgtcattttgcactctgcagAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG