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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttgtaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

Basic information

species Zea mays
transcript GRMZM2G064563_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G13760.2 (Glycine max), 3'ss of exon 4
---------gtatgcttaacccat-ctcatcagactgcgcataaccaaatatgcat-atgaaacctgtgtttgccttgtaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
          |||  || |    |  |||||      |   ||  |   |    ||  |    ||   |||    || ||  ||  ||  | ||  | |||||||||||||| || || ||||| |||||||||||  | ||||| || || |||||||| ||||| || ||||||||||| |||||||| |||||||| ||
cttattctgttatcatttatttttattcatctcttgtcttgtattcttgttcatattgtacttcccaagttcattttttactgcattctttctg--cctcagATGAAAAGATAGCCTTGCTGGGTGCCATACAGTCTCTCTTTGAAGGTTCAATGTACACCTTTGTGTTTCTATGGACTCCTGCATTGAGCCCAAATGATGA

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 4
--gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttgt--aacgctgtcca-----tttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
   ||| ||     | | |  |           |   |   ||| | | |  |   |||  || ||  ||  |  | |  | |     ||||  ||||||||||||| || || || ||||| || ||||||||  | ||||| || || |||||||| ||||| || || |||||||| |||||||| |||||||| ||
tcttattctgtgatcttttattttattcatctcttgtcttgtattcttgttcatattgtacttcccaagttcattgtttactacattctttgtgcttcagATGAAAAAATAGCCTTGCTGGGTGCTATACAGTCTCTCTTTGAAGGTTCAATGTACACCTTTGTGTTTCTGTGGACTCCTGCATTGAGCCCAAATGATGA

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 2
gtatgcttaacccatctcatcagactgcg-cataaccaaatatgcatatgaaacctgtgtttgccttgtaacgctgtccatttgatct--tcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
||     |    | |  | |  |  |  | ||||    ||||||  | ||   || |  ||   |||  |       || ||| ||    |||||||| ||||| |||||||| || || || |||||  ||||||| || ||||||||||| ||||| || || |||||||| || ||||| ||||| |||||
gtgaatctcttaccttaccttggtttttgacatactgtaatatgtctttgcttccagctttattcttccactaaccacctttttattaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgcct-----tgtaacgctgtccat--ttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                                      |  | || ||   |     ||    | |     | |    ||  || || || || ||||| |       | |||| |  || ||  ||  |  |||||||||||||||||||| ||||| || || |||||  | || || | ||| |||||||| ||||| ||||| ||||| |||||  | || ||||| || ||
gcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttctcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
--gtatgcttaacccatctcatcagactg----cgcataaccaaatatgcatatgaaacctgtgtttgccttgtaacgctgtc-catttgatct---tcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
   |||  |    |  |||  |  || |        ||      |  |   | |   |  | | |||   || |||   |||    ||| || |   |||||||| || || ||||| ||||| || ||||||||  | ||||| || || |||||||||||||| ||||| |||||||| || |||||||| ||||||||
atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattt-tctttttattttaatattgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 4
----gtatgcttaacccat---ctcatcagactgcg-cataaccaaatatgcatatgaaacctgtgtttgccttgtaacgctgtccatt-tgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
    || ||||   || ||    | |||   |||   | | | |   |  |  | |    ||| | || |   | ||    | |   |  ||   ||||||||| || ||||| || ||||| || || ||||| |||||||| ||||| ||||| || ||||| ||||| |||||||| ||  | || |||||||||||
cattgtttgctatcccaatgggtttatccatctgtttcctcatcttttcagttttttcctcctttcttggagctttagtattatgtttcatgtggttcagATGAGAAAATTGCGTTGCTGGGTGCAATTCAGTCGTTGTTTGAAGGCTCAATGTATACTTTTGTGTTCCTCTGGACTCCTGCTCTAAGCCCAAATGAAGA

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------------gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgt-ttgccttgtaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                                                                                      || ||||       |    | |||  | | ||     |  |  || |  ||  |    |  ||  |||| |   |||| | |  ||   ||||||| ||||| ||  |  |||| ||||| ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || || ||  |
gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtac--tgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtc-actgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------gtatgcttaacccatctcatcag-actgcgcataaccaaatatgcatatgaaacctg----tgtttgccttgtaacgctgtccat-----ttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                                                                        |||| |||||  | |   ||    | | | | |   |   | ||   |   |   |     |||  |  |||  |   |     |     ||| | | ||||||||||||||||  |  |||| || || || || ||||| || || |||||||| |||||||| ||||| ||||| ||||||||||||||  ||||  |
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtat-cttaatgctttagatttctatttctcctggacgcttgtgtgcagtgattgtaatattgtgagaattgggatcttacttgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
lower sequence: EFJ21113 (Selaginella moellendorffii), 3'ss of exon 4
gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttgtaacgctgtccatttgatctt---cagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                                       || || | | |   || | |         | |  | ||  || |||  |    |||||||||||||||  | || ||||| || || ||  | || ||||||||||||||||| || |||||||| ||||| || ||||||||||| || ||  |
--------------------------------------gtaagcttttcatgtctttatgcaagcgagagccttatct-ttggattctatgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
lower sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 4
gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttgtaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                            | | | |     |||  | | |  |  | |   ||||| |    || |  |||  || |  |||||||||||||||  | || ||||| || || ||  | || ||||||||||||||||| || |||||||| ||||| || ||||||||||| || ||  |
----------------------------gta-agcttttcatgtctttaatgcaagcgagagccttat----ctttggattctatgt--agATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA

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|32863387|gb|CF003069.1|CF003069
EST:     CAAGGACCTGATGGCCCAGTTCAAGGTTGCAGCTAAGGCGATCGCGTCAG                         ATGAAAAGATTGCATTACTGGGAGCCATACAGTCACTGTTTGAGGGCTCCA
genomic: CAAGGACCTGATGGCCCAGTTCAAGGTTGCGGCTAAGGCAATTGCGTCAGgtatgcttaa ... tgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCA
EST: gi|149086869|gb|EE176413.2|EE176413
EST:     CAAGGACCTGATGGCCCAGTTCAAGGTTGCGGCTAAGGCAATTGCGTCAG                         ATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCA
genomic: CAAGGACCTGATGGCCCAGTTCAAGGTTGCGGCTAAGGCAATTGCGTCAGgtatgcttaa ... tgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCA
EST: gi|211313230|gb|FL392892.1|FL392892
EST:     GCTAAGGCAATTGCGTCAG                         ATGAAAAGA-TGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCA
genomic: GCTAAGGCAATTGCGTCAGgtatgcttaa ... tgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCA

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), 43 (downstream exon)
Score: 55

GCTATCATAATGTCCTCATGGAGTGAAAACTACGGAGATCCATCTGAAAGCAAGGACCTGATGGCCCAGTTCAAGGTTGCGGCTAAGGCAATTGCGTCAGgtatgcttaa ... tgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 54

GCTATCATAATGTCCTCATGGAGTGAAAACTACGGAGATCCATCTGAAAGCAAGGACCTGATGGCCCAGTTCAAGGTTGCGGCTAAGGCAATTGCGTCAGgtatgcttaa ... tgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

GCTATCATAATGTCCTCATGGAGTGAAAACTACGGAGATCCATCTGAAAGCAAGGACCTGATGGCCCAGTTCAAGGTTGCGGCTAAGGCAATTGCGTCAGgtatgcttaa ... tgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

GCTATCATAATGTCCTCATGGAGTGAAAACTACGGAGATCCATCTGAAAGCAAGGACCTGATGGCCCAGTTCAAGGTTGCGGCTAAGGCAATTGCGTCAGgtatgcttaa ... tgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatgcatatgaaacctgtgtttgccttgtaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                                       tccattt  CT-rich tract
        atatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttgtaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA