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'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGATATTGGGTCTTGGTGATCTTGGGGTGCATGGTATTGGCATTGCTATTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaatggttctttagaactctaatttcagattattcccctctttcccatcttattttcagttccacctaaactggccaccttttgcagccaaat...

Basic information

species Zea mays
transcript GRMZM2G406672_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G406672_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g31380.1 (Oryza sativa), 5'ss of exon 5
CAGGATATTGGGTCTTGGTGATCTTGGGGTGCATGGTATTGGCATTGCTATTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaatggttctttagaactctaatttcagattattcccctctttcccatcttat--tttcagttccacctaaactggccaccttttgcagccaaat--
|||||||||||| || |||||||| ||||||||||||||||| ||||| |||||||| |||||| |||||||||||||||||||||||||||| || |||||        | | | | | | ||  ||     ||||| ||   ||||| ||  |||     ||  | ||  || |   | |  |   ||||| |   |  |  
CAGGATATTGGGCCTGGGTGATCTCGGGGTGCATGGTATTGGTATTGCCATTGGAAAGTTGGATCTATATGTTGCTGCTGCTGGAATAAATCCCCAGAGGgtaaaaacttttggtttatggtaccttaga---agattgttagactcttccctttctccctcttctaattttacatctcccgtgc-ttttttgtaatgactttt

upper sequence: GRMZM2G406672_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G24630.1 (Glycine max), 5'ss of exon 5
CAGGATATTGGGTCTTGGTGATCTTGGGGTGCATGGTATTGGCATTGCTATTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttg------aatggttctttagaactctaatttcagattattcccctctttcccatcttattttcagttccacctaaactggccaccttttgcagccaaat
||| || ||||| ||||| |||||||| || || || ||||||||||| ||||| ||  | ||| ||||||||||||||||||| |||||||||||||||||  | ||      |||| ||| |||    | |  ||||  | | |||   | ||    |  ||  | ||  ||          |    |  | |  ||       
CAGAATCTTGGGACTTGGAGATCTTGGAGTTCAAGGAATTGGCATTGCCATTGGGAAGCTTGATCTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGGgtacgctgttgctcaatgtttcattat--ttttcctttccaactgttcaggttttgataacattggtatct-ttatgttgtcggtaaggaaatatcccaattt---

upper sequence: GRMZM2G406672_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT2G13560.1 (Arabidopsis thaliana), 5'ss of exon 5
CAGGATATTGGGTCTTGGTGATCTTGGGGTGCATGGTATTGGCATTGCTATTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaatggttctttagaactctaatttcagattattcccctctttcccatcttattttcagttccacctaaactggccaccttttgcagccaaat
| |||| ||||||||||| ||||| || || ||||| ||||| |||||| | || ||  | |||||||||||||| || |||||||||||||||||| ||||   ||| |   |    ||      || ||||       || ||  ||| |  | | || |         | ||      |   ||  |  ||      
CCGGATTTTGGGTCTTGGAGATCTAGGTGTTCATGGAATTGGAATTGCTGTAGGGAAGCTTGATTTATATGTTGCCGCAGCTGGAATAAATCCTCAACGGgtac-ttgcaccatctaatattttcttattttc---cccatctccatttttctgtatgatgtgatacaattcttatgtgcacatgctggtttag------

upper sequence: GRMZM2G406672_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv15s0021g00500.t01 (Vitis vinifera), 5'ss of exon 5
CAGGATATTGGGTCTTGGTGATCTTGGGGTGCATGGTATTGGCATTGCTATTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaatggttctttagaactctaatttcagattattcccctctttcccatcttattttcagttccac-ctaaact--ggccaccttttgcagccaaat
||| |||||||||||||| |||||||| || || || ||||| ||||| ||||| ||  |||||||||||||||||||||||||||||||||||||||| || | ||     | | |  |   | ||  ||      ||      |       || | | |   |        || || |  ||| |   |   |  | ||| 
CAGAATATTGGGTCTTGGAGATCTTGGAGTTCAGGGCATTGGGATTGCAATTGGGAAGCTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGAgtatctt--cccgctttacatgtcacttgttcttatctaagtattttagatgaatatgactagaaaccatgttctgaattttggctagactgcccctctaaa-

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|76922708|gb|DV169132.1|DV169132
EST:     TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGG                         GTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCCTTA-
genomic: TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCC-TTAA
EST: gi|211078044|gb|FL102373.1|FL102373
EST:     TTGGAAAATGGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGG                         GTTCTTTCCTGTTATGATTGATGTCTGAAC
genomic: T-GGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTT-CCTGTTATGATTGATGTCGGAAC
EST: gi|149080135|gb|EE169155.2|EE169155
EST:     TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGG                         GTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCTTAAG
genomic: TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCTTAAG
EST: gi|78118566|gb|DV536950.1|DV536950
EST:     TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGG                         GTTCTTCCTGTTATGATTGATGTCGGAACGAACA-CGAGAAGCTCCTTAAG
genomic: TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCTTAAG
EST: gi|149077946|gb|EE166677.2|EE166677
EST:     TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGG                         GTTCTTCCTGTTATGATTGATGTC
genomic: TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTC
EST: gi|71438805|gb|DR819855.1|DR819855
EST:     TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGGATAAATCCTCAAAGG                         GTTCTTCCTGTTATGATTGATGTC
genomic: TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTC
EST: gi|71436416|gb|DR817466.1|DR817466
EST:     TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGG                         GTTCTTCCTGTTATGATTGAT
genomic: TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGAT
EST: gi|78125331|gb|DV543715.1|DV543715
EST:     TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGG                         GTTCTTCCTGTTATGATTGATGTCGGAGCGAACAACGAGAATCTCTTTAGG
genomic: TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCTTAAG
EST: gi|32941434|gb|CF046253.1|CF046253
EST:     TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGG                         GTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCGTAAG
genomic: TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCTTAAG
EST: gi|71417559|gb|DR804119.1|DR804119
EST:     TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGG                         GTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCTTAAG
genomic: TTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCTTAAG

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), 49 (downstream exon)
Score: 120

CAGGATATTGGGTCTTGGTGATCTTGGGGTGCATGGTATTGGCATTGCTATTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCTTAAGGATCCTCTTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 206

CAGGATATTGGGTCTTGGTGATCTTGGGGTGCATGGTATTGGCATTGCTATTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCTTAAGGATCCTCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

CAGGATATTGGGTCTTGGTGATCTTGGGGTGCATGGTATTGGCATTGCTATTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCTTAAGGATCCTCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

CAGGATATTGGGTCTTGGTGATCTTGGGGTGCATGGTATTGGCATTGCTATTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaa ... ttttttctagGTTCTTCCTGTTATGATTGATGTCGGAACGAACAACGAGAAGCTCCTTAAGGATCCTCTTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGATATTGGGTCTTGGTGATCTTGGGGTGCATGGTATTGGCATTGCTATTGGAAAATTGGATTTATATGTTGCTGCTGCTGGAATAAATCCTCAAAGGgtgtgttgaatggttctttagaactctaatttcagattattcccctctttcccatcttattttcagttccacctaaactggccaccttttgcagccaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA