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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactattatttgttatttttggtgggctgctgcctactgtattagtcactatggacattgacgtctatgcatttcttggcatggttcttttatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT

Basic information

species Zea mays
transcript GRMZM2G024690_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024690_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g49900.1 (Oryza sativa), 3'ss of exon 4
-tactattatttgttatttttggtgggctgctgcctactgtattagtcactatggacattgacgtctatgcattt-cttggcatggttcttttatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT
  | |||     | ||||  | ||           ||  |    ||| | | ||||  || || | |||   ||| | | |||| | |  || | |  ||||||||||||||||||||||||| || ||||||||||| ||||| |||||||||||||||||||||||||||
aaaatatctagagatattagttgttaatacaatagtagcgctaaagttaatttggatgttaacctttattttttttccttgcattggt--ttgactattcagAATGTGTAGAGCTTTAATGCCAGGAGATGAAGAAAGTATGAGCGATGAAGCTATTTGGGAGACACTTCCT

upper sequence: GRMZM2G024690_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G13040.1 (Glycine max), 3'ss of exon 4
tactattatttgttatttttggtgggctgctgcctactgtattagtcactatgga-cattgacgtctatgcatttcttggc--atggttcttttatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT
    || | |  | |    |   |      |   |  |||    | |  |||  | || | |  | | |||  ||  |  |  |   |  ||||||||  ||| |||||||  ||| ||||||| |||||||||||||  ||||||||||| ||||| ||||| || || |||
---gatgaatgttaaccccttcagaataattcattggtgtgggggcccatattcatcaattatttatctgccctttgtaaccaactatatttttattttgcagGATGTGTAAGGCTCTAATGCCAGGGGATGAAGAAAATATGAGTGATGAGGCTATATGGGAAACTCTCCCT

upper sequence: GRMZM2G024690_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 4
tactattatttgttatttttggtgggctgctgcctactgtattagtcactatggac-attgacgtctatgcatttcttggc--atggttcttttatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT
    || | |    |  | |   |      |    | |||   || |  |||  || | | |  | | | |  ||  |  |  |   |  ||||||||  ||| |||||||  ||| ||||||| ||||||| ||||| |||||||||||| ||||| ||||| || ||||||
---gatgaatgcgaacctcttcagcataattcatgagtgtgggagcccatattcaccaattatttatcttccctttataaccaactatatttttattttgcagGATGTGTAAGGCTCTAATGCCAGGGGATGGAGAAAACATGAGTGATGAGGCTATATGGGAAACTCTTCCT

upper sequence: GRMZM2G024690_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G68820.1 (Arabidopsis thaliana), 3'ss of exon 4
---tactattatttgttatttttggtgggctgctgcctactgtattagtcactatggacattgacgtctatgcatttcttggcatggttcttttatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT
   | | |||    | | |||||| |    | |  ||| || || || ||     | ||    ||   ||    ||| |||  |   ||| |        ||||||||| ||  |  | |||||||| ||||||||||  |||||||||||||| || ||||| |||||||||
gtattccattcaaagct-tttttgattttgttcacccttct-tactactcttagagtacgg-aacaattaaatcttttttgcaactattcctg-------cagAATGTGCAGGACGCTCATGCCTGGAGATGAAGAAACTATGAGTGATGAAGCCATATGGGAAACACTTCCT

upper sequence: GRMZM2G024690_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g04160.t01 (Vitis vinifera), 3'ss of exon 4
-----tactattatttg---ttatttttggtgggctgctgcctactgtattagtcactatggacattgacgtctatgcatttcttggcatggttcttttatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT
     | ||| | |||    ||||  |  |||  ||  | |  | | ||||    | | ||   ||   | || |   ||   |||  ||    | |||  |   |||||||||||  ||  ||||||| || |||||||||||||||||||||||||| || |||||||||||||||
ggctttgctactttttaactttatgctcagtgaactattcctcagtctatt--ctagt-tgattat--gcttcaacctataaattgatat---ccatttgctctacagAATGTGTAAGGCGCTAATGCCAGGAGATGAAGAAAGCATGAGTGATGAAGCAATATGGGAGACACTTCCT

upper sequence: GRMZM2G024690_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0011g02950.t01 (Vitis vinifera), 3'ss of exon 4
--tactattatttgttatttttggtgggctgctgcctactgtattagtcactatggacattgacgtctatgcatttcttggcatggttcttttatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT
  || || | |    |  | ||  |  |   |     |  |||  | | | | ||   | |   |  |  ||  |  ||  ||      | || | | | || |||||||  |||||||||||||| ||||| |||||||| ||||||||||| || |||||||| ||||||
tatattactttgcagttgtattacttagtgtcaagtaatagtaa-aataattctgtcaaattgtgcatcagc-ctgattaacaaatgcatgttttattttagGATGTGTAAGGCTTTAATGCCTGGAGATGATGAAAGCATTAGTGATGAAGCAATATGGGAGACCCTTCCT

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|148938797|gb|EC883136.2|EC883136
EST:     CTTCCCCTGTTGGCCTTTTGAAACAATAATCCCTTATTGACAATTTTTAG                         AATGTGTAGAGCTTTTATGC
genomic: CTTCCCCTGTTGGCCTTT-GAAGCAATAATCC-TTATTGACAATTTT-AGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGC
EST: gi|149070957|gb|EE159363.2|EE159363
EST:     TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAG                         AATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
genomic: TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
EST: gi|88756990|gb|DY541131.1|DY541131
EST:     TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAG                         AATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
genomic: TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
EST: gi|211453584|gb|FL021068.1|FL021068
EST:     TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAG                         AATGTGTAGAGCTTTAATGCCTGG
genomic: TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGG
EST: gi|148931986|gb|EC875260.2|EC875260
EST:     TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAG                         AATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
genomic: TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
EST: gi|91870315|gb|EB400812.1|EB400812
EST:     TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAG                         AATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
genomic: TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
EST: gi|78117592|gb|DV535979.1|DV535979
EST:     TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAG                         AATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
genomic: TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
EST: gi|149104180|gb|EE289614.2|EE289614
EST:     TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAG                         AATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
genomic: TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
EST: gi|211453580|gb|FL021064.1|FL021064
EST:     TCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTTAG                         AATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAG
genomic: TCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTT-AGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAG
EST: gi|211453582|gb|FL021066.1|FL021066
EST:     TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAG                         AATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC
genomic: TTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGC

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: 44 (upstream exon), 49 (downstream exon)
Score: 56

TTAGAAATCATCCATCTGTTGATCTGAAGATTGTGTTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 68

TTAGAAATCATCCATCTGTTGATCTGAAGATTGTGTTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 77

TTAGAAATCATCCATCTGTTGATCTGAAGATTGTGTTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

TTAGAAATCATCCATCTGTTGATCTGAAGATTGTGTTCCTTCCCCTGTTGGCCTTTGAAGCAATAATCCTTATTGACAATTTTAGgtaatcaatt ... tatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactatggacattgacgtctatgcatttcttggcatggttcttttatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT
          cattgac  putative branch site (score: 82)
                                       ttcttttatttgtc  putative PPT
                                       ttcttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactattatttgttatttttggtgggctgctgcctactgtattagtcactatggacattgacgtctatgcatttcttggcatggttcttttatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - ttttggt
- - - - - - - - - - - - -gctgctg
- - - - - - - - - - - - - - - - cctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatggt