Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtcttcttttttacttggtgaacgcagtgttagtttgtaatttatagcatgtcaaggaatctgatgaagtgcctgccatttttttatgtag

Basic information

species Zea mays
transcript GRMZM5G879882_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T03 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 5'ss of exon 12
GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtcttcttttt--------tacttggtgaac----gcagtgttagtttgtaatttatagcatgtcaaggaatctgatgaagtgcctgccatttttttatgtag-----------------------
||||| ||||||| ||| |||||||||||||||||||| || ||||||||   |||| |||||        | || | || ||    | |||| ||||||| | |   ||   | |  | | ||||||  |  | |||      | ||    ||                        
GATTACTGCAAGAACAAAAAGATGGAGATGACTATTAAGTATATAGgtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtac-tactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcag
















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|32858441|gb|CD998122.1|CD998122
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|74238195|gb|DT646109.1|DT646109
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|40334982|gb|CK369052.1|CK369052
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|37401035|gb|CF637880.1|CF637880
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|37382133|gb|CF627993.1|CF627993
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|4967240|gb|AI691913.1|AI691913
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|40336088|gb|CK370158.1|CK370158
EST:     GATTATTGCAAGATCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|76286570|gb|DV026138.1|DV026138
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|113703664|gb|EE681168.1|EE681168
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|4966450|gb|AI691306.1|AI691306
EST:     TAAGGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: TAAGGATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|120480265|gb|EH210787.1|EH210787
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTTT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|108954346|gb|EC365109.1|EC365109
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|86474334|gb|DY240704.1|DY240704
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|6540652|gb|AW225314.1|AW225314
EST:     GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAG                         ATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCT

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: 46 (upstream exon), 49 (downstream exon)
Score: 178

GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 161

GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 237

GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 118

GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtct ... ttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTATTGCAAGAGCAAGAAGATGGAGATGACTATTAAATACATAGgtaatcgtcttcttttttacttggtgaacgcagtgttagtttgtaatttatagcatgtcaaggaatctgatgaagtgcctgccatttttttatgtag

- - -  GCAAGA
- - - - - AGAGCA
- - - - - - AGCAAG
- - - - - -  GCAAGA
- - - - - - -  AAGAAG
- - - - - - - - - AAGATG
- - - - - - - - - - GATGGA
- - - - - - - - - - - TGGAGA
- - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - GAGATG