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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgttgttacactgatgttgatgaaaagcatcaataagagcagacccggaggctcccacatgagtggggtctaggtaagggataccgaagcaagc...

Basic information

species Zea mays
transcript GRMZM5G844195_T02
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 14
CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgttgttacactgatgttgatgaaaagcatca--ataagagcagacccgg-aggctcccacatgagtggggtctaggtaagggataccgaagcaagc
|||||||| || || |||||||||||||| || ||||| |||||||| ||||||||| ||||||||||||| | |||||||||| ||||||||   |  | ||  ||||| |||||| ||| |   ||  || |       | |   | | || |||||    |     | | |  | |||    |   |   
CTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATTCACATGTTGCACAATGATGACCATGAAGAGATGTTGAAGgtacacttgtattctactgaagttgattaaatgatgcagaattattttgtgctcattatgttctcacattttagtaacttcgtttcgtgatggttacata---

upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA17G37870.1 (Glycine max), 5'ss of exon 15
-CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgttgttacactgatgttgatgaaaagcatcaataagagcagacccggaggctcccacatgagtggggtcta-ggtaagggataccgaagcaagc
  ||||||||||||| || || ||||| ||||| ||||| || || ||||| |||||||| || |||||||| || || || ||| | |||||||         | |    |||| |||       ||||   ||   |  | || |  || |   | ||||     ||    | |    |  ||       
GGTTGATGAAGAAGATTTCAATGAGGAGCAAAATTCTGTCGCTCGCCTCATACACATGCTTCATAATGATGAACCAGAGGAAATGTTTAAggtaacg-------ataagtgtgttcatg------gtcaaattgaattgcactggtgtttctccattaagtgcttcatataacacgactcattgaccttca-

upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA14G40270.1 (Glycine max), 5'ss of exon 14
CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgttgttacactgatgttgatgaaaagcatcaataagagcagacccggaggctcccacatgagtggggtctaggtaagggataccgaagcaagc-----
 ||||||||||||| || || ||||| ||||||||||| || || ||||| |||||| | || ||||||||  | || || ||| | |||||||         | |    |||| ||        ||||   ||   |  | || |  || |   | ||||    ||   ||    | | |  |   | |     
GTTGATGAAGAAGATTTCAATGAGGAGCAAAACTCTGTTGCTCGCCTCATACACATGTTTCATAATGATGAATCAGAGGAAATGTTTAAGgtaacg-------ataagtgtgttcata------gtcaaattgaattgcactggtgtttctctattaagtg----cttcatataacacaactcattgaccttcag

upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 15
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 5'ss of exon 14
CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgttgttacactgatgttgat-gaaaagcatcaataagagcagacccggaggctcccacatgagtggggtctaggtaagggataccgaagcaagc-----
|||||||| || || || ||||| |||||||| ||||| || |||||||| |||||| |  |||||||||| || ||||| ||| |||||||||||  ||  | ||  | | |  || | | |  ||   |       ||  |  | | | | | ||  ||    ||    |||         || ||        
CTTGATGAGGAGGATTTCAAGGATGAACAAAATTCTGTCGCTCGTCTCATACACATGTTCTACAATGATGACCCCGAAGAAATGTTGAAGgtaattgatttgttcaaggttttctattgcacaatattgttt----ttgatgctaatgttacgaaatctgttcattcc--ttaaatctctttaaatcagttaaatt

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|31355991|gb|CD440348.1|CD440348
EST:     CGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG                         ATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTA
genomic: CGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgtt ... ggtctttcagATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTA
EST: gi|31353910|gb|CD438267.1|CD438267
EST:     CGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG                         ATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTA
genomic: CGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgtt ... ggtctttcagATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTA
EST: gi|31355451|gb|CD439808.1|CD439808
EST:     CGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG                         ATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTA
genomic: CGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgtt ... ggtctttcagATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTA
EST: gi|78088719|gb|DV517112.1|DV517112
EST:     CGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG                         ATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTA
genomic: CGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgtt ... ggtctttcagATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTA

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

CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgtt ... ggtctttcagATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTAACTTTCACTGTGCCTTCGTTAGTATTCTCTTCTCTTAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 82

CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgtt ... ggtctttcagATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTAACTTTCACTGTGCCTTCGTTAGTATTCTCTTCTCTTAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 139

CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgtt ... ggtctttcagATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTAACTTTCACTGTGCCTTCGTTAGTATTCTCTTCTCTTAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 146

CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgtt ... ggtctttcagATCTTATGTACTGTACAGAAGCATATACTTCAGGGAGGCCCCAAGCGTCTAACTTTCACTGTGCCTTCGTTAGTATTCTCTTCTCTTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAGgtaatttgttgttacactgatgttgatgaaaagcatcaataagagcagacccggaggctcccacatgagtggggtctaggtaagggataccgaagcaagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG