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'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatcaggaaatacagttcaatccttcttgttaacatagtaatctaacataaattttcaatcttatttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA

Basic information

species Zea mays
transcript GRMZM2G033619_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 3
gtagatcaggaaatacagttcaat-ccttcttgttaacatagtaatctaacataaattttcaatcttatttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA
||| |  ||||||||   || ||    |||  |  | |||  |     ||  |   ||| ||||||||||  |||||||||||||||||||||||||||||||||| |||||||| |||||| |||| ||||||||||||||||| ||||| || ||||||||||| |||||||| |
gtacaagaggaaatatttttgaaggttttcgggccagcattcttgctcaaagt---tttgcaatcttattgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATACTCATGAATGCAACTGACAAATCAAATAGAATGTTGCGGGCCAAATCGA

upper sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 4
gtagatcaggaaataca--gttcaatccttcttgttaacatagtaatctaacataaat--tttcaatcttat----ttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA
|||  |   ||| | |   ||||||||    |    ||  || |    |   || | |  ||| | | ||||    ||  | |||||||||||||||||||||||||||| ||||||||||| || || |||||  |  | |||||||| || || || ||| | ||| | ||||| || ||||
gtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATATTGGTTAATGCAACCGACAAGTCTAACCGTATGCTTCGTGCTAAGTCCA

upper sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 6
gtagatcaggaaataca--gttcaatccttcttgttaacatagtaatctaacataaat--tttcaatcttat----ttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA
|||  |    || | |   ||||||||    ||  |||  || |    |   || | |  ||| | | ||||    ||  | |||||||||||||||||||||||||||| |||||||||||||| ||||||||  |  | ||||||||||| ||||| ||| | ||| | ||||| || ||||
gtattttgttaacttctttgttcaatcaacatttataatttattttcttttgatcactcatttaattattatggtctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATACCTGAAGGCTATATTGGTTAATGCAACTGACAAATCTAACCGTATGCTTCGTGCTAAGTCCA

upper sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 4
-----gtagatcaggaaatacagttcaatc-----cttcttgttaacatagtaatctaacataaattttcaatcttatttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA
      || ||    |||||   ||| ||       ||||| | ||   || |  ||||||    |||| | | | | |     ||||||| ||||||||||| ||||||||||| ||||| ||||| || || ||  | |||||||| ||||| || || ||| | ||| | ||||||||| |||
gtattatatattttaaaatatgcttccattatggttttcttataaatg-agcagcctaacac---ttttgagtatcaat-----agGAACATTTCCAAAAATACTATGATGCAGTTATGCCTTACCTAAAAGCAATATTGATGAATGCCACTGACAAGTCTAACCGCATGCTTCGTGCCAAAGCCA

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|22545771|gb|BU098145.1|BU098145
EST:     TGCAAGAAGCTGCTTTAACTGCTTTAGCATCAGCAGCAGATTCTTCTCAG                         GAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATT
genomic: TGCAAGAAGCTGCTTTAACTGCTTTAGCATCAGCAGCAGATTCTTCTCAGgtagatcagg ... atttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATT
EST: gi|26558109|gb|CA830344.1|CA830344
EST:     AACTGCTTTAGCATCAGCAGCAGATTCTTCTCAG                         GAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATT
genomic: AACTGCTTTAGCATCAGCAGCAGATTCTTCTCAGgtagatcagg ... atttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATT

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: 85

ACTGGGAACCAAATGGTGCAAGAAGCTGCTTTAACTGCTTTAGCATCAGCAGCAGATTCTTCTCAGgtagatcagg ... atttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 39

ACTGGGAACCAAATGGTGCAAGAAGCTGCTTTAACTGCTTTAGCATCAGCAGCAGATTCTTCTCAGgtagatcagg ... atttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 43

ACTGGGAACCAAATGGTGCAAGAAGCTGCTTTAACTGCTTTAGCATCAGCAGCAGATTCTTCTCAGgtagatcagg ... atttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 45

ACTGGGAACCAAATGGTGCAAGAAGCTGCTTTAACTGCTTTAGCATCAGCAGCAGATTCTTCTCAGgtagatcagg ... atttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatccttcttgttaacatagtaatctaacataaattttcaatcttatttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA
                      atctaac  putative branch site (score: 45)
                                         tcttattt  putative PPT
                atagtaatctaacata  TA-rich tract