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'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   		36  
 5'  3'   		37  
 5'  3'   		38  
 5'  3'   		39  
 5'  3'   		40  
 5'  3'   
41  
 5'  3'   		42  
 5'  3'   		43  
 5'  3'   		44  
 5'  3'   		45  
 5'  3'   		46  
 5'  3'   		47  
 5'  3'   		48  
 5'  3'   		49  
 5'  3'   		50  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaacttgcaaaaccactgttctgttgttgtagacccttgcagccgctagattgttgacccttgcaaaaccaccattagcaacaagattcttcgcaaagccttttttttcttggtaaccaacattgttcggttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACTCACTGGGGTGATGCTGCATCGAACAATCCAAATCCATCTACTCACTCAG

Basic information

species Zea mays
transcript GRMZM2G068755_T03
intron # 46
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 48
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 47
gtagaacttgcaaaaccactgttctgttgttgtagACCCTTGCAGCCGCTAGATTGTTGACCCTTGCAAAACCACCATTAGCAACAAGATTCTTCGCAAAGCCTTTTTTTTCTTGGTAACCAACATTGTTCGGTTGTTGTAGACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACTCACTGGGGTGATGCTGCATCGAACAATCCAAATCCATCTACTCACTCAG
                                            |     | | |     |  |||     ||||       |||||  |     | | | |||||||||  ||| ||      |||||      ||| ||||||||||| || ||||||||| |||| ||||| ||  ||||||| |||||||||||||||||||| |  || || |||||||| ||||| ||||| ||| 
--------------------------------------------gtaaaaaaaatacatccttttgttgttccac-------aacaaactgtcatggacatcctttttttaattgatact----attgt------gttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACTCACTGGGGTGATGCAGGGTCCAATAATCCAAACCCATCAACTCATTCAA
















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|93014606|gb|EB640126.1|EB640126
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAG                         ACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
EST: gi|32834298|gb|CD973976.1|CD973976
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAG                         ACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
EST: gi|67021414|gb|CO450163.1|CO450163
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAG                         ACCCTTGCAGCCGCTAGAAATGT-GACGCCATCGGGGCCTATGGGTCAAAC
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAA-TGTTGACGCCATCGGGGCCTATGGGTCAAAC
EST: gi|37424588|gb|CF650027.1|CF650027
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAG                         ACCCATGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
EST: gi|32838771|gb|CD978452.1|CD978452
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAG                         ACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
EST: gi|67015335|gb|CO444084.1|CO444084
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAG                         ACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
EST: gi|32834018|gb|CD973696.1|CD973696
EST:     ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAG                         ACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
genomic: ATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACT
EST: gi|71317537|gb|DR795494.1|DR795494
EST:     TGCTGACCCTTCAGCCA-TAATTCTAGCATACATTGATCTCAATCTCCAG                         ACCCTTGCAGCCGCTAAAATGTTGACG
genomic: TGCTGAACCT-CAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAATGTTGACG

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: 141

GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACTCACTGGGGTGATGCTGCATCGAACAATCCAAATCCATCTACTCACTCAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 45

GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACTCACTGGGGTGATGCTGCATCGAACAATCCAAATCCATCTACTCACTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 64

GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACTCACTGGGGTGATGCTGCATCGAACAATCCAAATCCATCTACTCACTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 88

GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttg ... gttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACTCACTGGGGTGATGCTGCATCGAACAATCCAAATCCATCTACTCACTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcttcgcaaagccttttttttcttggtaaccaacattgttcggttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACTCACTGGGGTGATGCTGCATCGAACAATCCAAATCCATCTACTCACTCAG
                          tggtaac  putative branch site (score: 88)
                ttttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaacttgcaaaaccactgttctgttgttgtagacccttgcagccgctagattgttgacccttgcaaaaccaccattagcaacaagattcttcgcaaagccttttttttcttggtaaccaacattgttcggttgttgtagACCCTTGCAGCCGCTAGAATGTTGACGCCATCGGGGCCTATGGGTCAAACTCACTGGGGTGATGCTGCATCGAACAATCCAAATCCATCTACTCACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC