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'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgattgatctactcactttaaaaatactaaattggatctcgagttcatattgtccatctttcagtttttagtcttgcaaataaattatttgcag...

Basic information

species Zea mays
transcript GRMZM5G844195_T02
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844195_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 20
CAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgattgatctactcact--ttaaaaatactaaattggatctcgagttcatattgtccatctttcagtttttagtcttgcaaataaattatttgcag
||||||||||||| ||||| ||||| ||||||||||| || ||||| |||||||| ||||| |||||||| |||||||| || |||||||||||||||||||||  |  |     |||| | |  || ||| |  || | | | | |    | | || | | || |||| ||||  |  |||||||||| || | || | | 
CAGCAAAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCATGTTCACACCTTTTCTGGACTGACGACCAAGACGGAATAATGGATGGTGAAAGgtaaacttctaagcatactgatttgttgaaacttgtagactagttatgccatccgtaattttcaacttttagttcgt--tcttgcaaatgaaatgttaggac

upper sequence: GRMZM5G844195_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G37870.1 (Glycine max), 5'ss of exon 21
-CAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgattgatctactcactttaaaaatactaaattggatc--tcgagttcatattgtccatctttcagtttttagtcttgcaaataaattatttgcag-
 ||||||| ||| | ||||| |||||||| ||||||||||| ||||| || || ||||| ||||||  |||||| ||||||||||| |  ||||| |||||||| | || |  |  ||||||  ||      | ||   ||  |   |||  |||||    ||  |   ||   || |  | |   |||||| | || | |   
TCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGAGAAAggtatgctggtaaa--tactcaaattggtttaattaggatgatttgatcggtttcatgc-atctttgcctcttcttatgttttctgaaataa-tgatctccttt

upper sequence: GRMZM5G844195_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA14G40270.1 (Glycine max), 5'ss of exon 20
CAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgattgatctactcactttaaaaatactaaattgg--atctcgagttcatat-tgtccatctttcagtttttagtcttgcaaataaattatttgcag-
||||||| ||| | ||||| |||||||| ||||||||||| ||||| || || ||||| ||||||  |||||| ||||||||||| |  ||||| |||||||| | || |  | || ||||  ||      ||||   ||   || |||  |||||   | |    || | | || |  || ||   ||  ||| || | |   
CAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGAGAAAGgtatgctggt--aactgctcaaattggtttaactaggatgattatatcggtttcatgcatctttgcctcttacttat--gttttctgaaataatgatcttcttt

upper sequence: GRMZM5G844195_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 5'ss of exon 20
CAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgattgatctactcactttaaaaatacta-aattggatctcgagttcatatt----gtccatctttcagtttttagtcttgcaaataaattatttgcag
||||||| ||| | ||||| |||||||||||| ||||||| ||||| ||||| ||||||||||||  ||| || |||||||| || | |||||| |||||||    |  || | |  ||||  | | | || ||| |||| | |   | | || ||||    ||  |   | ||  |||     |  ||| ||||  | |     
CAGCAAAGCTTTTAAAGAAACCTGATCAATGCAGAGCAGTTTATGCATGTTCCCATCTTTTTTGGGTTGACGATCAAGATGGCATTAAGGATGGAGAAAGgtgctttccttcagcccctca--tgatagatcctagaatttgcttgtgtggtcttatttcatgtttactctgcatctttggtgttctcaattaaagaaataa---

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|32865287|gb|CF004969.1|CF004969
EST:     ATCTTTTTTGGACTGATGACCAAGAT-GTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: ATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|9952706|gb|BE639169.1|BE639169
EST:     TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|24768924|gb|CA404053.1|CA404053
EST:     TGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTG-TTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: TGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|31356855|gb|CD441212.1|CD441212
EST:     TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|67012219|gb|CO440968.1|CO440968
EST:     TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|211321315|gb|FL043264.1|FL043264
EST:     TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|18964320|gb|BM660937.1|BM660937
EST:     TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|31355991|gb|CD440348.1|CD440348
EST:     CACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAAATCGCAA-TGCTGCTCAA
genomic: CACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGG-TGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAA-TCGCAAATGCTGCTCAA
EST: gi|24769517|gb|CA404646.1|CA404646
EST:     CAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: CAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|211321314|gb|FL043263.1|FL043263
EST:     TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|31353910|gb|CD438267.1|CD438267
EST:     TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTT
genomic: TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTT
EST: gi|67014984|gb|CO443733.1|CO443733
EST:     TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|32865123|gb|CF004805.1|CF004805
EST:     ATCTTTTTTGGACTGATGACCAAGAT-GTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: ATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|148965444|gb|EE016250.2|EE016250
EST:     GGACTGATGACCAAGATGGTATAATGGATGGTGAAAGG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAAC
genomic: GGACTGATGACCAAGATGGTATAATGGATGGTGAAA-Ggtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAAC
EST: gi|211321316|gb|FL043265.1|FL043265
EST:     TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|211462641|gb|FL447919.1|FL447919
EST:     TGATGACCCAAGAGGGTATAATGGA-GGGGAAAAG                         GGTTCT-CTTTGTTTGAAGCGT-CCTTGAGAATCGCAAATTCTGCTCAAC
genomic: TGATGA-CCAAGATGGTATAATGGATGGTG-AAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAAC
EST: gi|211321311|gb|FL043260.1|FL043260
EST:     TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|211321310|gb|FL043259.1|FL043259
EST:     TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: TCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
EST: gi|32865124|gb|CF004806.1|CF004806
EST:     ATCTTTTTTGGACTGATGACCAAGAT-GTATAATGGATGGTGAAAG                         GGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA
genomic: ATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACA

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: 47 (upstream exon), 49 (downstream exon)
Score: 155

CAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACAGATGGCTAGTGCTACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 120

CAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACAGATGGCTAGTGCTACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 154

CAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACAGATGGCTAGTGCTACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 130

CAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgat ... tttgtttcagGGTTCTCCTTTGTTTGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACAGATGGCTAGTGCTACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTGAAAGgtaagatgattgatctactcactttaaaaatactaaattggatctcgagttcatattgtccatctttcagtttttagtcttgcaaataaattatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG