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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttgaattttagaagtcagaactcatgttgatgaacttcctgaggttattgggggctaatttattgtttctatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG

Basic information

species Zea mays
transcript GRMZM5G846548_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846548_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g11500.1 (Oryza sativa), 3'ss of exon 8
gtaagtt--tttgaattttagaagtcagaactcatgttgatgaacttcctgaggttattgggggctaatttattgttt--ctatgt-tctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG
|||||    |||  ||  |  |  ||| |||   | || |      |  | |  |  |||   | ||| | ||| |||  |||| | | ||||||||||||||||||||||||||||||||||  |||| ||||||||||||||||| ||||||||||||||||| |||||||||
gtaagcggatttacatgatgaatttcataacc--ttttaaattttcttttaaaatgtttgttcgttaactaattatttgactatctgtatagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCGTTAACCCAGCATTTTGCACTTGCCAATAATGCAGCTGATATATCTGCAAAG

upper sequence: GRMZM5G846548_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G07190.2 (Glycine max), 3'ss of exon 8
-----------gtaagtttttgaattttagaagtcagaactcat--gttgatgaacttcctgaggttattgggggctaatttattgtttctatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG
            |   || ||  ||||    | | | |  | ||  ||  |   | ||  |    || ||     |||    | | |   ||||  |||||||||||||| ||||| || |||||||||||  | || ||||||||||| |||    ||||||| || ||||| |||||||||
attaagacttttttttttcttttatttcctgattgatattttatttgtgtactgattttttttccttttttctctctatcaaaatatgattatgaactagCTGGTGTTGCAAGTGGTGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAG

upper sequence: GRMZM5G846548_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G13010.1 (Glycine max), 3'ss of exon 4
---------gtaagtttttgaattttagaagtcagaactcatgt---tgatgaacttcctgaggttat-tgggggctaatttattgtttctatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG
          |   || ||  ||||    | | | |  | || |   |  | |  ||  |  | |||| |     |||    | | |   ||||  |||||||||||||| |||||||| |||||||||||  | || ||||||||||| |||    ||||||| || ||||| |||||||||
ttaaggcattttttttcttatatttcctgattgatagtttatttgtgtactaatttttttttgtttatattttctctatcaaaatatgattatgaactagCTGGTGTTGCAAGTGGAGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAG

upper sequence: GRMZM5G846548_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G13770.2 (Arabidopsis thaliana), 3'ss of exon 7
----gtaagtttttgaattttagaagtcagaactcatgttgatgaacttcctgaggttattgggggctaatttattgt--ttctatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG
    |||   |||      | | |  |  ||| | | |     |   |   |      || ||    ||| || ||    |  |   |  ||||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| |||  | | |||||||| ||||| ||||| |||
gtgcgtatcatttcttgcatcaaacatt-gaagttaagacttcggtttggattgatacatcggtttttaacttttttcaatcttggctattagCTGGTGTTGCAAGTGGAGCAACCAGAGCAGCTCTAACACAGCACTTTGCTCTTCAAGACAATGCAGCGGATATATCTGCTAAG

upper sequence: GRMZM5G846548_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv01s0011g00500.t01 (Vitis vinifera), 3'ss of exon 8
----------------gtaagtttttgaattttagaagt-cagaactcatgttgatgaacttcctgaggttattgggggctaatttattgtttctatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG
                | || |  ||    |  | |||   |   | |||  || |||  || || |  | |       |||||||     |  |      ||||||||||||| ||||||||||||||||| ||| | || || |||||||| |||  ||||||||| || ||||| ||||| |||
tattgtcagtggaattgaaaatacttctgctgaataagaataatgcacattgtgttgatatttctca--tca--aaaatctaattttacactcttcaaaattagCTGGTGTTGCAAGTGGAGCAACTAGAGCTGCATTGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAG

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|18654521|gb|BM499326.1|BM499326
EST:     TTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCA                         CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCAC
genomic: TTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCAgtaagttttt ... tatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCAC
EST: gi|18654522|gb|BM499327.1|BM499327
EST:     TTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCA                         CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCAC
genomic: TTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCAgtaagttttt ... tatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCAC
EST: gi|18649151|gb|BM497970.1|BM497970
EST:     TTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCA                         CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCAC
genomic: TTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCAgtaagttttt ... tatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCAC
EST: gi|88755251|gb|DY539392.1|DY539392
EST:     TTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCA                         CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCAC
genomic: TTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCAgtaagttttt ... tatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCAC
EST: gi|18648891|gb|BM497710.1|BM497710
EST:     AATGTGCTTAGGCAGCCTGTCTAGGTCATTCA                         CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCAC
genomic: AATGTGCTTAGGCAGCCTGTCTAGGTCATTCAgtaagttttt ... tatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCAC

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: 103

GAATGTTGATGGATCTTTTGAGCCCTCTGTTTCCTTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCAgtaagttttt ... tatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 100

GAATGTTGATGGATCTTTTGAGCCCTCTGTTTCCTTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCAgtaagttttt ... tatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

GAATGTTGATGGATCTTTTGAGCCCTCTGTTTCCTTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCAgtaagttttt ... tatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

GAATGTTGATGGATCTTTTGAGCCCTCTGTTTCCTTCATCGTTGATAGTTATAATGTGCTTAGGCAGCCTGTCTAGGTCATTCAgtaagttttt ... tatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgatgaacttcctgaggttattgggggctaatttattgtttctatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG
                            ggctaat  putative branch site (score: 51)
                                      ttgtttct  putative PPT
                               taatttattgtttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttttgaattttagaagtcagaactcatgttgatgaacttcctgaggttattgggggctaatttattgtttctatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG