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

GCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccctatgcttcacctagtattcatagcctctccccttctgctttccatttttttttgtaactgaccacttgtcaatcggcag

Basic information

species Zea mays
transcript GRMZM2G115245_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 26
GCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccctatgcttcacctagtattcatagcctctccccttctgctttccatttttttttgtaactgaccacttgtcaatcggcag
||||||||||  ||||||||||| |||||||||||||| ||||| ||||| || ||||| ||||||||||||||||||||||| ||||| || ||| |   |  | |  | |  |||||  |   || |  | ||   ||   |     ||||  || ||                   
GCATATGAGAGGTCAGAAGATCCTATTTATGTTTTGGATAATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAAgtatgtccagaacacatttcttgatattcgaaaattcgcttcctccaattctaacaaactttt--aattgctag---------------

upper sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA06G16110.1 (Glycine max), 5'ss of exon 26
GCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccctatgcttcacctagtattcatagcctctccccttctgctttccatttttttttgtaactgaccacttgtcaatcggcag
|||||||||| |||||| ||||| || |||||  | || || || |||||||| |||||||| ||||| |||||||| ||||||||||||||| ||    ||   || |     | ||   |   |||||     || ||||   | ||| ||         ||  ||           
GCATATGAGAGATCAGAGGATCCTATCTATGTGCTAGAGAACAACATACCCATAGATCCTCATTACTATCTTGAGAATCAAATTAGCAAGgttggtttattag--tttattagatgttttgaatttctcca---atgttttctgctatttattagcttcattcatgtgcag--------

upper sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA04G38800.2 (Glycine max), 5'ss of exon 10
GCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccctatg-cttcacctagtattcatagcctctccccttctgctttccatttttttttgtaactgaccacttgtcaatcggcag
||||| ||||||||||| ||||| || |||||| | || || || ||||| || |||||||| ||||| |||||||| ||||||||||||||| ||    |||| ||| |     | ||       |||   ||  || || |  || ||| ||         ||  |  ||        
GCATACGAGAAATCAGAGGATCCTATCTATGTTCTAGAGAACAACATACCAATAGATCCTCAGTACTATCTTGAGAATCAAATTAGCAAGgttggt---ttatgactttattggatgttttggatttct---ctaatgtttactgttctttattagcttcattcatattgcag-------

upper sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S54_271V6.1 (Physcomitrella patens), 5'ss of exon 26
GCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccctatgcttcacctagtattcatagcctctccccttctgctttccattt-----ttttttgtaactgaccacttgtcaatcggcag--------
|| |||||||| ||||||||||| || ||||||||||| |||||||| || |||||||| ||||||||| | || |||||  | || |||||  ||   | ||| |     |     | | || |   |   || || ||| || ||     || ||    || ||||   |||  |  |||          
GCGTATGAGAAGTCAGAAGATCCAATCTATGTTTTGGAGAATAATATTCCGATTGATCCACAATACTACTTGGAAAACCAGCTGAGTAAGgtgcgtcttcaatgatgtgtttttggcttaaagtcagactt-ttatggtttgcacttggaaattattctctacagacc-tgtgtgcaggggcgtttaatgtt

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|32930209|gb|CF035021.1|CF035021
EST:     ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAG                         CCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG
genomic: ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccc ... caatcggcagCCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG
EST: gi|32932138|gb|CF036950.1|CF036950
EST:     ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAG                         CCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG
genomic: ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccc ... caatcggcagCCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG
EST: gi|211441104|gb|FL033100.1|FL033100
EST:     ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAG                         CCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG
genomic: ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccc ... caatcggcagCCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG
EST: gi|32931064|gb|CF035876.1|CF035876
EST:     ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAG                         CCACCTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG
genomic: ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccc ... caatcggcagCCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG
EST: gi|32931909|gb|CF036721.1|CF036721
EST:     ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAG                         CCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG
genomic: ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccc ... caatcggcagCCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG
EST: gi|32932752|gb|CF037564.1|CF037564
EST:     ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAG                         CCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG
genomic: ATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccc ... caatcggcagCCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTG

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: 140

GCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccc ... caatcggcagCCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTGCTTCATGGAAGCCACACCAGATCTGTTTCAATCTCAACTCCTTCCAATA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 30

GCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccc ... caatcggcagCCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTGCTTCATGGAAGCCACACCAGATCTGTTTCAATCTCAACTCCTTCCAATA


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 15

GCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccc ... caatcggcagCCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTGCTTCATGGAAGCCACACCAGATCTGTTTCAATCTCAACTCCTTCCAATA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 20

GCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccc ... caatcggcagCCACTTTTGAGGATCTTTGAGCCAATTCTGAAGAATGCCAGCAAAGAGTTGCTTCATGGAAGCCACACCAGATCTGTTTCAATCTCAACTCCTTCCAATA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAGgtttgtgccctatgcttcacctagtattcatagcctctccccttctgctttccatttttttttgtaactgaccacttgtcaatcggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG