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'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggccacctgaaaaaacaacaaatatgacaactacaaggtcaaatcacatatacgactcatacattttctgttctttgtgatctccttccaatgtgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTG

Basic information

species Zea mays
transcript GRMZM2G376731_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os04g59494.4 (Oryza sativa), 3'ss of exon 19
aaggccacctgaaaaaacaacaaatatgacaactacaaggtcaaatcacatatacgactcata-cattttctgttctttgtgatctccttc-caatgtgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTG
|| | ||  | ||    ||   |   | ||    |   ||  |     |  |  | |     | ||       || |  | |||| | ||  | |  ||||| |||||||| |||||||||||||  | |||||||  ||||||||||| ||| | ||||| ||  |||| |||||||||||||| ||||||||||||||||
aaagtcaattcaatcggcattgatcttcactggaatctgg--atgctgctgactccatctgcatcaaagaaacttatacgggatcactttttctacatgcagGTTGATCCTGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGTGCATTGGATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTG

upper sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 19
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 19
aaggccacctgaaaaaacaacaaatatgacaactacaaggtcaaatcacatatacgactcatacattttctgttctttgtgatctccttc----caatgtgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTG
  |   | |||     |  | |  ||   |   || || || || |   ||  || |   ||| | ||  |     |||   | |   |     || | | |||||||||||| || |||||||||    |||||||| ||| || ||||| || ||  | ||| | ||||||||||||||||||||||||||   ||| || |
-tgcttagctggtcgcattatatgtagctccttta-aaagttaatttgaatg-acaaga-atatagttgttacaacttgcagtttttgttttgacacttttcagATTGATCCTGCTTCAGCTGGTGTTCAGTATGATAAAGAGTTTATTGTATGCTCTCTCGACTTGCTGTCTGGACTTGCAGAAGGTCTTGGTAGTGGGATAG

upper sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 19
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 3'ss of exon 19
aaggccacctgaaaaaacaacaaatatgacaactacaaggtcaaatcacatatacg-actcatacattttctgttctttgt---gatctccttccaatg--tgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTG
    |||   |        | | || |    ||  |||| | ||||  | | | |   ||| ||  ||||   ||  |||     |  |   | | ||   ||||| ||||||||    |||||| ||     ||||||| ||||||||||||||| || |||||| | || || || |||||||||||||||||   ||| ||||
----ccatgagcgttgctga-agattttttcacatcaagataaaatt-cttgtccatgctcttatcttttagtttgcttgcctgaaggttggtgctataattgcagGTTGATCCTCTGTCAGCTGCTGTTCAATATGATAAAGAATTCATTGTTTGCTCTTTGGACTTGCTCTCAGGGCTTGCAGAAGGTCTTGGTAGTGGAATTG

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|91872776|gb|EB402733.1|EB402733
EST:     CAGTGTTTCAAAGGTGCATCAATCTTATCCAATCGCAACAGTTGGCAAAG                         ATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGT
genomic: CAGTGTTTCAAAGGTGCATCAATCTTATCCAATCGCAACAGTTGGCAAAGgtctgtctaa ... caatgtgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGT




















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), 49 (downstream exon)
Score: 137

GCATTGGGACCAGGATTTGCTCAGTTTGCGGAACCAGTGTTTCAAAGGTGCATCAATCTTATCCAATCGCAACAGTTGGCAAAGgtctgtctaa ... caatgtgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 113

GCATTGGGACCAGGATTTGCTCAGTTTGCGGAACCAGTGTTTCAAAGGTGCATCAATCTTATCCAATCGCAACAGTTGGCAAAGgtctgtctaa ... caatgtgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

GCATTGGGACCAGGATTTGCTCAGTTTGCGGAACCAGTGTTTCAAAGGTGCATCAATCTTATCCAATCGCAACAGTTGGCAAAGgtctgtctaa ... caatgtgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 79

GCATTGGGACCAGGATTTGCTCAGTTTGCGGAACCAGTGTTTCAAAGGTGCATCAATCTTATCCAATCGCAACAGTTGGCAAAGgtctgtctaa ... caatgtgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacatatacgactcatacattttctgttctttgtgatctccttccaatgtgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTG
                                     tctccttcc  CT-rich tract
               atacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggccacctgaaaaaacaacaaatatgacaactacaaggtcaaatcacatatacgactcatacattttctgttctttgtgatctccttccaatgtgcagATTGATCCTACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTG

- -gccacct
- - - - - gaaaaaa
- - - - - - - - -caacaaa
- - - - - - - - - - - - - - - aactaca
- - - - - - - - - - - - - - - - - - - - - -aatcaca