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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtagtttctttttccaacatataatgttcttccacgttacaaaatctttctgattagatgttctttttcttcccatag

Basic information

species Zea mays
transcript GRMZM2G020976_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g40030.1 (Oryza sativa), 5'ss of exon 5
GCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtagtttct---ttttccaacatataatgttcttccacgttacaaaatctttctgattagatgttctttttcttcccatag
||||||||||||||| |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| | |   || |   |||| | ||||| |||    ||| |   |||| |  |||||| |  ||  ||| | |||  |   |   
GCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttcattttcagttttgccacatacaatcccattctaaactacatag-ctttctaaccagcagttttgttttgttttag--

upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv11s0016g05710.t01 (Vitis vinifera), 5'ss of exon 5
GCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtagtttctttttccaacatataatgt-tcttccacgtta-----caaaat--ctttctgattagatgttctttttcttcccatag------
||||||||||| ||| ||||||||||  |   ||| ||||||||||| |||||||| ||||||   |||||||| ||||||||| | |||   ||||| ||||  | |   ||||| |  |  |  ||  |   |  || | | ||     |||| |  ||||||  | | ||||  | ||| |  | || |      
GCTGGAGCTCGGGACCTGTCATTTGACTCCTATGGCTATGCTATTGTTTTTGTGGCAAACATTTGTACAGCTGTATATCTTGCTTCTATATCTCGTATTGgtactattttgttcttatgtcttctcatgtttcattctctatggtaacgttcaaagtttctttctattgatatgtggtatttttctcaattgtctcag
















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|74233566|gb|DT641480.1|DT641480
EST:     TGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAG                         GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
genomic: TGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
EST: gi|31353270|gb|CD437627.1|CD437627
EST:     TGTGGCCAACATTACGACAGCTGTTTATCTTGCTACCATAAACCGTATAG                         GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
genomic: TGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
EST: gi|71767957|gb|DR965894.1|DR965894
EST:     TGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCCTAAACCGTATAG                         GGAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGGTCTTG
genomic: TGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGGTCTTG
EST: gi|78115508|gb|DV533896.1|DV533896
EST:     ACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAG                         GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
genomic: ACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
EST: gi|71420100|gb|DR805010.1|DR805010
EST:     TGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAG                         GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
genomic: TGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
EST: gi|31355902|gb|CD440259.1|CD440259
EST:     TGTGGCCAACATTACGACAGCTGTTTATCTTGCTACCATAAACCGTATAG                         GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
genomic: TGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
EST: gi|148947455|gb|EC892886.2|EC892886
EST:     TGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAG                         GAAAATCTAGTCGCCTTAATAGCTTTGGCCTGATGTGGTACCATG
genomic: TGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
EST: gi|89760089|gb|DY688655.1|DY688655
EST:     TGTGGCCAACATTACAACAGCTGTTTATCTTGTTACCATAAACCGTATAG                         GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG
genomic: TGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG

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), 45 (downstream exon)
Score: 63

GCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 124

GCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

GCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 104

GCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtag ... cttcccatagGAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtagtttctttttccaacatataatgttcttccacgttacaaaatctttctgattagatgttctttttcttcccatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT