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

...gctacttggtctatcaaattataactccatagcagatttctagtgaagtacctatacacctttgagtgctaatattattttttcctcctgaaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGG

Basic information

species Zea mays
transcript GRMZM2G100639_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 3
gctacttggtctatcaaattataactc----catagcagatttctagtgaagtacctatacacctttgagtgc-taatattatt--ttttcctcctgaaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGG
       || |||||| || || ||||    | | || |  | ||| |  |      | |  | ||| |     || |  || |  | ||   | | |||||  |||| ||  | || ||||| ||||||||||||||||| ||||  |||||||  ||||| |    |||||| |||||||||||||||||||||||||| |||||
-------ggcctatcacatcattactctgtgcctggctgcctgctacttcacagttcagaatcatttaaagatatattgctaatgctattttacttaaaaaattcagGTTCACTAGTAAGGCCGAAAGTTGTTAAGAGTGTTCACTATTGCCCTGCTACTGGAGGTACTCTCTCACGTGAATACAGGGACATCACATCTTTCGTAGG
















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|211158410|gb|FL068715.1|FL068715
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
EST: gi|211498655|gb|FL137520.1|FL137520
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
EST: gi|211158409|gb|FL068714.1|FL068714
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
EST: gi|211159999|gb|FL068726.1|FL068726
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGNCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
EST: gi|211158412|gb|FL068717.1|FL068717
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
EST: gi|30306471|gb|CD001144.1|CD001144
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
EST: gi|32806452|gb|CD958686.1|CD958686
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTA
EST: gi|18450616|gb|BM428894.1|BM428894
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGCTAAGAGTGTCCACTTCTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
EST: gi|211158408|gb|FL068713.1|FL068713
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
EST: gi|211158418|gb|FL068723.1|FL068723
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
EST: gi|211160000|gb|FL068727.1|FL068727
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGNCCACTTCTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
EST: gi|74233767|gb|DT641681.1|DT641681
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
EST: gi|211159998|gb|FL068725.1|FL068725
EST:     GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAAT                         GCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA
genomic: GTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGA

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: 309

GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGG


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

GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 25

GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 20

GGCTTCTCGGGTCCGTTCGGGTTCCACAGGGTCACGCCCAGGGATCTCATGTCCTCCTTCATCGGCACCATGGTCTGCGTTGAGGGCATCGTCACCAAATgtaacggctc ... aaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtacctatacacctttgagtgctaatattattttttcctcctgaaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGG
                     tgctaat  putative branch site (score: 20)
                                ttttttcctcctga  putative PPT
                     tgctaatattattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctacttggtctatcaaattataactccatagcagatttctagtgaagtacctatacacctttgagtgctaatattattttttcctcctgaaaaaaacagGCTCGTTGGTTAGGCCAAAAGTTGTTAAGAGTGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGG

-ctacttg