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

gtatggacgtttgctactacttctttagttctgatgatatgttcttgcttccagtttgtgcttgcatggaactcactgctcactgttctttcaattttgttacaagtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTCTAATGCATCTGATGCAGAACCTGAGAAACACCAGAGCAGTAGTCACCAT

Basic information

species Zea mays
transcript GRMZM2G464000_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G464000_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 10
gtatggacgtttgctactacttctttagttctgatgatatgttcttgcttccagtttgtgcttgcatggaactcactgctcactgttctttcaattttgttacaagtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTCTAATGCATCTGATGCAGAACCTGAGAAACACCAGAGCAGTAGTCACCAT
|||||  |  || |   ||  | ||| |   | |    | ||| |   ||     || || | |     |  ||  |  |  |    | | |  | ||  | ||||| | |||||||| |||||||||||||||||||| ||| ||||   | ||||||| ||||| |||||  | || |||||| |||||||||||||||  ||||| ||||||
GTATGAGCTGTTACCGTTAACTATTTGGCCATCACCTGAAGTTAT-ATTTTTGACTTCTG-TGGAGCACAGTTCCTTCATTTCCCCCCCTCC--TGTTACTGCAAGTTTTCACAGGTATGAGCTGTGCTTCAGTGGAGAAAAGGCTCGTCTTGTTGGATCAAGCTCCAATGCGGCAGACGCAGAAACTGAGAAACACCAGAATAGTAGCCACCAT
















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|211146181|gb|FK958445.1|FK958445
EST:     GCTAGACTGAAGAAAGGAGAAGTAATAYATTTGGAGACACATTTTAATAG                         GTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTC
genomic: GCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAGgtatggacgt ... gtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTC
EST: gi|58029867|gb|CX725294.1|CX725294
EST:     GCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAG                         GTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGGTATTGGATCGAGCT
genomic: GCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAGgtatggacgt ... gtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGG-TATTGGATCGAGCT
EST: gi|211146180|gb|FK958444.1|FK958444
EST:     GCTAGACTGAAGAAAGGAGAAGTAATATATTTKGAGACACATTTTAATAG                         GTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTC
genomic: GCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAGgtatggacgt ... gtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTC
EST: gi|211146178|gb|FK958442.1|FK958442
EST:     TAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAG                         GTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTC
genomic: TAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAGgtatggacgt ... gtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTC
EST: gi|78077940|gb|DV506360.1|DV506360
EST:     GCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAG                         GTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTC
genomic: GCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAGgtatggacgt ... gtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTC

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: 44 (upstream exon), 49 (downstream exon)
Score: 270

GTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACTTTATACTTCTGCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAGgtatggacgt ... gtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTCTAATGCATCTGATGCAGAACCTGAGAAACACCAGAGCAGTAGTCACCAT


Block sizes: 8 (upstream exon), 49 (downstream exon)
Score: 148

GTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACTTTATACTTCTGCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAGgtatggacgt ... gtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTCTAATGCATCTGATGCAGAACCTGAGAAACACCAGAGCAGTAGTCACCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 163

GTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACTTTATACTTCTGCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAGgtatggacgt ... gtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTCTAATGCATCTGATGCAGAACCTGAGAAACACCAGAGCAGTAGTCACCAT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 221

GTATAAGCATTGTGGCAGACAAGGGATTGAAAAAGTCACTTTATACTTCTGCTAGACTGAAGAAAGGAGAAGTAATATATTTGGAGACACATTTTAATAGgtatggacgt ... gtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTCTAATGCATCTGATGCAGAACCTGAGAAACACCAGAGCAGTAGTCACCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcatggaactcactgctcactgttctttcaattttgttacaagtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTCTAATGCATCTGATGCAGAACCTGAGAAACACCAGAGCAGTAGTCACCAT
                tgctcac  putative branch site (score: 221)
                                              tctccac  putative PPT
                            tttcaattttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggacgtttgctactacttctttagttctgatgatatgttcttgcttccagtttgtgcttgcatggaactcactgctcactgttctttcaattttgttacaagtctccacagGTACGAGCTGTGCTTCAGTGGAGAGAAGCCTCGGGGTATTGGATCGAGCTCTAATGCATCTGATGCAGAACCTGAGAAACACCAGAGCAGTAGTCACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG