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

...gtgctctgctgtggtattcctaagatttgtgcagagagcaaccatgcgcatattaccagccatcctacggtggatcttatgcagcatatcttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG

Basic information

species Zea mays
transcript GRMZM2G051004_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 11
---gtgctc-tgctgtggtatt-cctaagatttgtgcagagagcaaccatgcgcatattaccagccatcctacggtggatcttatgcagcatatcttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG
   | | || |||  | |||    || |   || ||    | ||    |||   | |||   |   ||| |      ||| |||  ||  |  | | | || |||||| ||||||||||||||||| ||||||||||| || |||||||| ||||| || ||||||||||| || ||||||||| | ||
actgcggtcatgcacttgtaccgtctgaagattctgtgatgtgcctgtatgta-acattgtga---atcttttatcagat-ttactcataagctgtgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG

upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 11
----gtgctctgctgtggtattcctaagatttgtgcagagagcaaccatgcgcatattaccagccatcctacggtggatcttatgcagcatatcttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG
    ||    |||| |  | ||  |  | |     |  |  ||    ||     | | |||         |          | |||  | |      | |  |||   || ||||||||  |||| ||||| || ||||| |||||||||||||| ||||| || ||||| |||||||||||||| ||
gtatgtctattgct-ttttgtttttttgctccaccctcattgctgtgattgttctgtaaccttttgcttgatttctatgactttgctac-tgaaaaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGAATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG

upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 11
gtgctctgctgtggtattcctaagatttgtgcagagagcaaccatgcgcatattaccagccatcctacggtggatcttatgcagcatatctttt------ttccagGGCG-GCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG
  |     || | |  ||  |    ||||  |      |  |  ||    |  |   |   | | |  | | ||| || |    | |  ||  |      |   | ||   || ||||||||  |||| |||||||| ||||| |||||||||||||| ||||| || ||||| |||||||||||||| ||
--gtatgtctattgcgttttttttttttggtctccactctgctgtgattgttctgt-actaaccttttgcttgat-ttctatgactttgctactgaaaaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG

upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 11
-------gtgctctgctgtggtattcctaagatttgtgcagagagcaaccatgcgcatattaccagccatcctacggtgg-------atcttatgcagcatatcttttttccagGGCG-GCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG
        |      || |     ||     || | |  |   | | | ||||| || | ||  |   |||| |   |         |||||   |     || |       | ||   || ||||||||  || | || ||||||||||| ||||| || ||||| ||||| |||||||||||||||||||| || ||
gtatactctctctctctctctctctctctctatctatctatctatctatcatgccca-agtatgatttatcccaaaatattaaaattatctttctctttgaatttccaactaaagGTATGCCTCAGAGGGGCCATTGAAGGGTATTCTTGGATACACGGATGAGGATGTTGTCTCCAATGATTTTGTTGGTGACTCAAG

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|211015683|gb|FL453044.1|FL453044
EST:     TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAA                         GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
genomic: TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
EST: gi|148928089|gb|EC872534.2|EC872534
EST:     TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAA                         GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
genomic: TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
EST: gi|37397668|gb|CF636141.1|CF636141
EST:     TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAA                         GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
genomic: TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
EST: gi|67025324|gb|CO454073.1|CO454073
EST:     TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAA                         GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
genomic: TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
EST: gi|40337147|gb|CK371217.1|CK371217
EST:     TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAA                         GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
genomic: TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
EST: gi|84977532|gb|DW475954.1|DW475954
EST:     TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAA                         GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
genomic: TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
EST: gi|30306629|gb|CD001302.1|CD001302
EST:     GCCTCCTATGATGATGTGAAAGCAGCCATCAA                         GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
genomic: GCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
EST: gi|31997624|gb|CD661686.1|CD661686
EST:     TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAA                         GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
genomic: TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
EST: gi|148944446|gb|EC889561.2|EC889561
EST:     TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAA                         GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA
genomic: TGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGA

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: 39 (upstream exon), 47 (downstream exon)
Score: 161

GCATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGACTTGACATGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG


Block sizes: 39 (upstream exon), 35 (downstream exon)
Score: 33

GCATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGACTTGACATGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG


Block sizes: 39 (upstream exon), 42 (downstream exon)
Score: 44

GCATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGACTTGACATGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 238

GCATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGACTTGACATGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa ... ttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgcatattaccagccatcctacggtggatcttatgcagcatatcttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG
                                       catatcttttttcc  CT-rich tract
                                        atatctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctctgctgtggtattcctaagatttgtgcagagagcaaccatgcgcatattaccagccatcctacggtggatcttatgcagcatatcttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG

- - tctgctg
- - - - - - - - - - - - - -tgtgcag
- - - - - - - - - - - - - - - - - - - - - catgcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcagc