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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggttactccattatatctgtgtgagttgtcatgggtctggatgttctgtagaacacatttttttgtgaatttcag

Basic information

species Zea mays
transcript GRMZM2G098039_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098039_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os05g01470.2 (Oryza sativa), 5'ss of exon 8
AGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggttactccattatatctgtgtgagttgt-----catgggtctggat--gttctgtagaac---acatttttttgtgaatttcag--------
||| |||||||||| ||| |||||||| |||||||| || |||||||||||| | |||||||||||||| |||||||||||||| ||||||||||||||||||||||  || |||  || | | || ||||||  |     ||| |  | | ||  |||  |   | |    |  |  |||   | | || |        
AGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgtaccttaatttctctcttttctgtgagtgagtcttgtgcacattgaccagaatttgtttggcgcatctgagctctactttagtagtctctgtcatcttc

upper sequence: GRMZM2G098039_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA12G28490.1 (Glycine max), 5'ss of exon 8
AGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtacct--tggttactccattatatctgtgtgagttgtcatgggtctggatgt-tctgtagaa-----cacatttttttgtgaatttcag----------
 |||||||||||||  ||||| |||||    |||||| |||||||||||||| | ||  ||||||| || | ||| ||||||||||||| |||| ||||||||     | |  |  || |  | | | |   | |||       | | | ||  ||||||  |     |  || | ||   ||| | ||           
TGAGAATGCTCTTCGCTTGTTTTCACCTCGCCTTGCAGTTGTTGATGAACATCTGACTCGACACTTACCTAGGCAGTGGTTAACATCTTCAGCACTTGAGgtatggaataggcatgccttggtcttttttgaacttgattaatattttgttgcatctgtattattatcccaatgtgttgaagaaatgcaattatgtgaac

upper sequence: GRMZM2G098039_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv12s0035g02060.t01 (Vitis vinifera), 5'ss of exon 1
AGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggttactccattatatctgtg---tgagttgtcatgggtctggatgttctgtagaacaca--tttttttgtgaatttcag-------------
 ||||||||||||||||| ||||||||    ||||||||||||||||||||| | ||  ||||  | || |  || ||||||||||| ||   ||||||||||          | || |     | |    ||  || | ||  |||      |      ||    |  ||||||| |   |   |              
TGAGAATGCTCTTCAATTATTCTCACCCCGTCTTGCAATTGTTGATGAACATCTGACTTGACATCTTCCAAGACAGTGGTTAACATCCTTGAAAATTGAGgtatggcataatttgcaatgctcttatactttgtatttttatatgtccaagcttcaccatgattttaatttttttttttggtactaaatttattgcacat

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|20507255|gb|BQ279551.1|BQ279551
EST:     ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAG                         GGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
genomic: ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
EST: gi|21809459|gb|BQ667777.1|BQ667777
EST:     ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAG                         GGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
genomic: ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
EST: gi|23199735|gb|BU582300.1|BU582300
EST:     ATTTAACCAGACACTTGCCCAAGCAACGGTTAACATCTTTAGCAATTGAG                         GGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
genomic: ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
EST: gi|20208173|gb|BQ134262.1|BQ134262
EST:     ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAG                         GGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
genomic: ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
EST: gi|87155600|gb|DY400389.1|DY400389
EST:     ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAG                         GGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
genomic: ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
EST: gi|20802934|gb|BQ293984.1|BQ293984
EST:     ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAG                         GGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
genomic: ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
EST: gi|26456508|gb|CA828091.1|CA828091
EST:     CCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAG                         GGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
genomic: CCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
EST: gi|22549094|gb|BU101295.1|BU101295
EST:     ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAG                         GGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA
genomic: ATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCA

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: 148

AGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCACCACGCCAATCAGATTTACTGATTGAGTTGATCAGGAAGCTGCAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

AGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCACCACGCCAATCAGATTTACTGATTGAGTTGATCAGGAAGCTGCAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 319

AGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCACCACGCCAATCAGATTTACTGATTGAGTTGATCAGGAAGCTGCAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

AGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggt ... tgaatttcagGGAAGAGCAGATTGTAATCACGCCGATGGTACAGTTACTGTAATTGAGGCACCACGCCAATCAGATTTACTGATTGAGTTGATCAGGAAGCTGCAGCCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggttactccattatatctgtgtgagttgtcatgggtctggatgttctgtagaacacatttttttgtgaatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA