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'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatatctgaaattcttgtgcacttctttgggcaagacgttatgcatttattcttctaatttaatatttttttgcctattgcactttcacgcatgc...

Basic information

species Zea mays
transcript GRMZM5G804064_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G804064_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 5'ss of exon 15
AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatatctgaaattct-tgtgcacttctttg--ggcaagacgttatgcatttattc---ttctaatttaatatttttttgcctattgcactttcacgcatgc
||||||||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||| | ||||||||| ||||||| |   ||||||||||||||     || ||||| | | |  | |||||||  | |||   |  |   |  ||| |   |||||  |    | || |  ||||  |||    |   ||||| 
AGAAAATATGATAGCTCATAAGGATGAGATATACTCAAGACCAAAGAGAACCTGGTTTGCTACTGAGAAGGAAAAGAAACTTTTGGCAAAGGCTGCTAAAgtaagttcgccttaaattgtatatatatttctttgatgccaaattgccaattacatatgcaaattctagctctcaaattgt--gcctgctgcctgct---gcatg-

upper sequence: GRMZM5G804064_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv18s0001g14540.t01 (Vitis vinifera), 5'ss of exon 15
AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatatctgaaattcttgtgcacttctttgggcaagacgttatgcatttat-tcttctaatttaatatttttttgcctattgcactttcacgcatgc-
 ||||| ||||| || ||||||||||| || |||||||| || || |||||||||||||| || |||| ||| ||||||  | ||| |   || || || ||||    || |   |   ||||    || ||||          || |  | ||| |  | |  | ||   ||| | ||    |||  | ||  |  || | 
TGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAAAGgtaatttcatattgcaccattgt-tgtttatttgtattcatttgtaagtctatatataatgttgtatatgttttgtctgtgagttg-gcatttccatattct
















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|32836593|gb|CD976271.1|CD976271
EST:     CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAA                         GAATCTTTGGGTCAAGGTAAGAGTAC
genomic: CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGTAC
EST: gi|32837990|gb|CD977668.1|CD977668
EST:     CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAA                         GAATCTTTGGGTCAAGGTAAGAGT
genomic: CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGT
EST: gi|47962731|gb|CN845440.1|CN845440
EST:     CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAA                         GAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAATTATTAGTGCTAAGCAG
genomic: CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAATTATTAGTGCTAAGCAG
EST: gi|33091483|gb|CF051477.1|CF051477
EST:     CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAA                         GAATCTTTGGGTCAAGGTAAGAGTACCTC
genomic: CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGTACCTC
EST: gi|37391010|gb|CF632744.1|CF632744
EST:     GAAGCTTTTGGTAGCAGCTGCTAAA                         GAATCTTNGGGTCAAGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGCAG
genomic: GAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAATTATTAGTGCTAAGCAG
EST: gi|21390142|gb|BQ528191.1|BQ528191
EST:     GGAAAAGAAGCTTTTGGTAGCAGCTGCTAAA                         GAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGCAG
genomic: GGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAATTATTAGTGCTAAGCAG
EST: gi|26457191|gb|CA828774.1|CA828774
EST:     CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAA                         GAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGCAG
genomic: CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAATTATTAGTGCTAAGCAG
EST: gi|13149411|gb|BG319733.1|BG319733
EST:     CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAA                         GAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGCAG
genomic: CCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAATTATTAGTGCTAAGCAG

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), 48 (downstream exon)
Score: 94

AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAATTATTAGTGCTAAGCAGGCTGAAGACCTCCGTCTGAAGGAGAAAAAGAGACGAGAGCATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAATTATTAGTGCTAAGCAGGCTGAAGACCTCCGTCTGAAGGAGAAAAAGAGACGAGAGCATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAATTATTAGTGCTAAGCAGGCTGAAGACCTCCGTCTGAAGGAGAAAAAGAGACGAGAGCATGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 41

AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatat ... ttccatcaagGAATCTTTGGGTCAAGGTAAGAGTACCTCTGGAATTATTAGTGCTAAGCAGGCTGAAGACCTCCGTCTGAAGGAGAAAAAGAGACGAGAGCATGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTAAAgtaagcatatctgaaattcttgtgcacttctttgggcaagacgttatgcatttattcttctaatttaatatttttttgcctattgcactttcacgcatgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT