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

CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcacttacacattttatgaatttgatggattttttccttacataaatccattaaatggtaaaatttttgtag

Basic information

species Zea mays
transcript GRMZM2G164265_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 3
CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcacttacacattttatgaatttgatg----gattttttccttacataaatccattaaatggtaaaatttttgtag
 |||||||||||||| ||||||||||||||||||||||| || ||||||||| ||||||| ||||||||| ||   || ||||||||||||||||||||||||||     || | |   ||| | |||| ||     || |  |  | |||| ||| || |  |      |   | |||||
TATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgtttgctctctaaatagaatat-attttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtag

upper sequence: GRMZM2G164265_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 3
CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcacttacacattttatgaatttgatggattttttccttacataaatccattaaatggtaaaatttttgtag-------------
||  |  || |||||||||||||| |||||||||||||| || ||||||||  |||||||   ||||||  |||   | || || ||||||||   ||||||     | |  || ||||| | ||    ||  |  ||||||    || | ||  || |    |   ||||     |             
CAAGATAGAAAGGAAGTTAGGTAAGGGTGGTTTTGGTCAAGTGTATGTTGGCAGAAGGGTAAGTGGTGGCACTGAAAGAACGGGACCTGATGCGCTTGAGgt--actatt--caaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatgctatttaaagggattcgcataacag
















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|148937187|gb|EC881368.2|EC881368
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|67020152|gb|CO448901.1|CO448901
EST:     GGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|149102516|gb|EE188222.2|EE188222
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|28909993|gb|CB331203.1|CB331203
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|18654924|gb|BM499729.1|BM499729
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAANCAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|18661950|gb|BM501665.1|BM501665
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|148950416|gb|EC895983.2|EC895983
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
EST: gi|78113587|gb|DV531978.1|DV531978
EST:     GTCGAGGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCCATCGAA-CAGTAAAGGATG
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGC-ATCGAAACAGTAAAGGATG
EST: gi|148950557|gb|EC896134.2|EC896134
EST:     GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAG                         GTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT
genomic: GTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCT

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), 47 (downstream exon)
Score: 235

CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 187

CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 174

CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 164

CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcact ... atttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcacttacacattttatgaatttgatggattttttccttacataaatccattaaatggtaaaatttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC