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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggccttcagccatgtgaattgtgaactctgcaattcttccaccattattactaaacatgatttatgggatttgcgataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAAGATATTGCTGATGACCGGCTTCAGCTTTGGATTGGTCGCAACGCACAAG

Basic information

species Zea mays
transcript GRMZM2G126266_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126266_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g70320.1 (Oryza sativa), 3'ss of exon 15
gtaggcctt-cagccatgtgaattgtgaactctgcaattcttccaccattattactaaacatgatttatgggatttgcgataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAAGATATTGCTGATGACCGGCTTCAGCTTTGGATTGGTCGCAACGCACAAG
|||  |||| |||| ||||||| | | ||       |||| ||||      ||| ||    |||||||||| || |    | ||| |||||||||||||||||||||||||||||||| |||||||||||  |||||||||| |||||||| || ||||||||| | |||||||||||||| |||  ||
gtaaacctttcagcgatgtgaactatcaa-------attcatccat-----ttattacgtgtgatttatggaatatatattgaatgcagGCATGGCTTATATACTTCTGGAGAAGAGCTAAAACTCATGGCATTGAGGAAGACATTGCTGAAGAACGGCTTCAGTTCTGGATTGGTCGCAATGCAGTAG

upper sequence: GRMZM2G126266_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA10G44630.1 (Glycine max), 3'ss of exon 15
--gtaggccttcagccatgtgaattgtgaactctgc----aattcttccaccattattact-aaacatgattt--atg-ggatttgcgataaatt--cagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAAGATATTGCTGATGACCGGCTTCAGCTTTGGATTGGTCGCAACGCACAAG
  |  | | || |  |   ||  |       ||||     || | |        ||||||| |||||||  ||  ||| | |||| |  |   |   ||||| ||||| | ||| || ||||||||||||||| |||||||| | ||||| || |||||||| || || |||| | |||||||| |||| |  |  ||  
aaggtgacatttactctcatggttctcactgtctgactagaaatgtgtgctttgtattactgaaacatgccttccatgtgaatttactcttcgtggacagGCTTGGCTGACATATTTTTGGAGAAGAGCCAAAGCTCATGGTATAGAGGAGGAAATTGCTGAAGAACGTCTTCGGTTTTGGATTAGTCGGAGTGGGCATT

upper sequence: GRMZM2G126266_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT5G23700.1 (Arabidopsis thaliana), 3'ss of exon 14
-----------------------------------------------------------gtaggccttcagccatgtgaattgtgaactctgcaattct-tccaccattattactaaacatgattt-atgggatttg-cgataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAAGATATTGCTGATGACCGGCTTCAGCTTTGGATTGGTCGCAACGCACAAG
                                                               |     |   ||  | ||  ||   |  | || |   |  | |   || | |    ||||    | |  |||||   |||||| |||||||||||||| ||||||||| | ||||||||    ||| |||| || ||||| ||||| ||||| ||  | ||| ||||||   |||| |  | |  | 
gtagtttctttatgcctataatttcataactataaggttataatgtgacattttgttacaagagatggtaattattggtatattgtggttggtaactaaatttatcgcgatgaatcttgatgaaccgacgttatttggttataaatgcagGCATGGCTTATGTACTTCTGGGGTAGAGCCAAGTTGCATAGTGTGGAAGAAGACATTGCAGATGAACGTTTCCAGTTTTGGACCAGTCGTAGTGAAGGAA

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|60343443|gb|DN210416.1|DN210416
EST:     ATCTTAGCCCAGAAGAGGCTGAAGATGTTAGCTTTAAGCAG                         GCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA
genomic: ATCTTAGCCCAGAAGAGGCTGAAGATGTTAGCTTTAAGCAGgtaggccttc ... ataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA
EST: gi|211038527|gb|FL455207.1|FL455207
EST:     GCTGAAGATGTTAGCTTTAAGCAG                         GCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA
genomic: GCTGAAGATGTTAGCTTTAAGCAGgtaggccttc ... ataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA
EST: gi|37381602|gb|CF627697.1|CF627697
EST:     ATCTTAGCCCAGAAGAGGCTGAAGATGTTAGCTTTAAGCAG                         GCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA
genomic: ATCTTAGCCCAGAAGAGGCTGAAGATGTTAGCTTTAAGCAGgtaggccttc ... ataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA
EST: gi|211120830|gb|FL155533.1|FL155533
EST:     ATCTTAGCCCAGAAGAGGCTGAAGATGTTAGCTTTAAGCAG                         GCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA
genomic: ATCTTAGCCCAGAAGAGGCTGAAGATGTTAGCTTTAAGCAGgtaggccttc ... ataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA
EST: gi|71324576|gb|DR798987.1|DR798987
EST:     GAAGATGTTAGCTTTAAGCAG                         GCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA
genomic: GAAGATGTTAGCTTTAAGCAGgtaggccttc ... ataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA
EST: gi|71324574|gb|DR798986.1|DR798986
EST:     TTAGCTTTAAGCAG                         GCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA
genomic: TTAGCTTTAAGCAGgtaggccttc ... ataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAA

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: 41 (upstream exon), 49 (downstream exon)
Score: 147

ATCTTAGCCCAGAAGAGGCTGAAGATGTTAGCTTTAAGCAGgtaggccttc ... ataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAAGATATTGCTGATGACCGGCTTCAGCTTTGGATTGGTCGCAACGCACAAG


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 74

ATCTTAGCCCAGAAGAGGCTGAAGATGTTAGCTTTAAGCAGgtaggccttc ... ataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAAGATATTGCTGATGACCGGCTTCAGCTTTGGATTGGTCGCAACGCACAAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 72

ATCTTAGCCCAGAAGAGGCTGAAGATGTTAGCTTTAAGCAGgtaggccttc ... ataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAAGATATTGCTGATGACCGGCTTCAGCTTTGGATTGGTCGCAACGCACAAG


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 95

ATCTTAGCCCAGAAGAGGCTGAAGATGTTAGCTTTAAGCAGgtaggccttc ... ataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAAGATATTGCTGATGACCGGCTTCAGCTTTGGATTGGTCGCAACGCACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattcttccaccattattactaaacatgatttatgggatttgcgataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAAGATATTGCTGATGACCGGCTTCAGCTTTGGATTGGTCGCAACGCACAAG
                  tactaaa  putative branch site (score: 95)
             attattactaaacatg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggccttcagccatgtgaattgtgaactctgcaattcttccaccattattactaaacatgatttatgggatttgcgataaattcagGCATGGCTTATATACTTCTGGAGAAGAGCCAAAACTCATGGTGTTGAGGAAGATATTGCTGATGACCGGCTTCAGCTTTGGATTGGTCGCAACGCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT