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

...cttaaaggaactttcatgtttatctttctgcggctgtgaggagttcaatttggatcctgactattctgtctgaaggaatttcgatacatttctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT

Basic information

species Zea mays
transcript GRMZM2G023798_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g04710.1 (Oryza sativa), 3'ss of exon 6
cttaaaggaactttcatgtttatctttctgcggctgtgaggagttcaatttggatcctgactattctgtctgaaggaatttcgatacat---ttctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT
  || |  |  | || | | |||||| ||           | ||| |||   ||||  || | |||| |||||| |  |||   |       || |  ||||||||||||||||||| ||||| |||||||| || ||||| || |||||||||||||| ||||| |||||||||| |||| ||| ||||||||| | |||||
--tacataatttatcctatgtatcttgcttttatcactttgtgtttaata-agatctggatttttctttctgaaagtttttttttttgggtattgtattgcagGAAGATCTGTACTATCCACATCCATTCGTGCAGGATGTATTATGGGCCACTCTCCACAAATTTGTTGAACCAGCTATGTTGCGTTGGCCTGGGAACAAAT

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 7
--cttaaaggaactttcatgtttatctttctgcggctgtgaggagttcaatttggatcctgactattctgtctgaaggaatttcgatacatttctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT
     | |  || || ||| |  || ||||     |  |    | ||   ||    |     ||||  || |  | ||   |||  | ||||  |  ||||||||||||||||||||||||| ||||| || || ||| |  | ||| |  | ||| | ||| | ||||||||  || | |||||||||||||| |  || |
tctgcagaaaaatttgcatttccatttttccattaccctttttattttggttcttgtttctcctatattggc--atggggattcattgcattaattttgcagGAAGATCTGTACTACCCACATCCATTGGTGCAGGATATACTTTGGACATCCCTCGACAAAGTTGTTGAACCTATTCTAATGCATTGGCCTGGGAAAAAGT
















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|21331674|gb|BQ487055.1|BQ487055
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|211505955|gb|FL017761.1|FL017761
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|211505957|gb|FL017763.1|FL017763
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|211505958|gb|FL017764.1|FL017764
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGNACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|9733396|gb|BE512253.1|BE512253
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|211505959|gb|FL017765.1|FL017765
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGGGNTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|211505960|gb|FL017766.1|FL017766
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT

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: 47 (upstream exon), 49 (downstream exon)
Score: 121

TGGCCGAATCACACCACTTCTGTTGGAATTAAGGAAGGAACTTTTCAAAGACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 72

TGGCCGAATCACACCACTTCTGTTGGAATTAAGGAAGGAACTTTTCAAAGACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

TGGCCGAATCACACCACTTCTGTTGGAATTAAGGAAGGAACTTTTCAAAGACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

TGGCCGAATCACACCACTTCTGTTGGAATTAAGGAAGGAACTTTTCAAAGACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttggatcctgactattctgtctgaaggaatttcgatacatttctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT
         tcctgac  putative branch site (score: 85)
                                           tttctgct  putative PPT
                                      atacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaaaggaactttcatgtttatctttctgcggctgtgaggagttcaatttggatcctgactattctgtctgaaggaatttcgatacatttctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT

- -aaaggaac
- - - - - - - catgttt
- - - - - - - - - - - - - - -gcggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - gatcctg