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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaacaatttatagcattttctctgccttatttctaattgttttcaaggttagtatgagttgcatattttttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGTCGAGACTTTGTAG

Basic information

species Zea mays
transcript GRMZM5G870572_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G870572_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g25060.1 (Oryza sativa), 3'ss of exon 3
---------------gtttgaacaatttatagc--attttctctgccttatttctaattgttttcaaggttagtatgagttgca-----tat---tttttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGTCGAGACTTTGTAG
                 || |||  | | | |   | ||||| | | | || |  | ||||||      ||   |  | ||| |     |||   ||||||  | ||| |||||||||||| ||||||||||||||||||  |||||| |||| || ||| ||||||||||
gtataggcaattctaccttaaactttatcttgttgaatttctattcatgatctacatttgtttctgtcattgagaaaaattgaaatttctatgtgttttttctttagGGTGGAGGCTACATGTTTGAGTTTGACAATGTTACTAACCGCGACCTATCTCGTGACTTTGTAG
















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|211184536|gb|FL153191.1|FL153191
EST:     AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAG                         GCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
genomic: AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
EST: gi|211184539|gb|FL153194.1|FL153194
EST:     AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAG                         GCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
genomic: AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
EST: gi|211184530|gb|FL153185.1|FL153185
EST:     AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAG                         GCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
genomic: AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
EST: gi|211184534|gb|FL153189.1|FL153189
EST:     AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAG                         GCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
genomic: AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
EST: gi|211184537|gb|FL153192.1|FL153192
EST:     AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAG                         GCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
genomic: AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
EST: gi|148959670|gb|EC905590.2|EC905590
EST:     AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAG                         GCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
genomic: AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
EST: gi|211184535|gb|FL153190.1|FL153190
EST:     AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAG                         GCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
genomic: AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
EST: gi|211184538|gb|FL153193.1|FL153193
EST:     AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAG                         GCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
genomic: AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
EST: gi|89756532|gb|DY686536.1|DY686536
EST:     AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAG                         GCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
genomic: AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
EST: gi|211184531|gb|FL153186.1|FL153186
EST:     AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAG                         GCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
genomic: AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
EST: gi|211184529|gb|FL153184.1|FL153184
EST:     AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAG                         GCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT
genomic: AAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGT

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: 34

GTCACAAGTTCAATAAAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGTCGAGACTTTGTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

GTCACAAGTTCAATAAAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGTCGAGACTTTGTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

GTCACAAGTTCAATAAAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGTCGAGACTTTGTAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 41

GTCACAAGTTCAATAAAGTAGAGGGTAACAAAGCAGCATTATTGAACCTTTCAAAAGAAGACAAGgtttgaacaa ... tttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGTCGAGACTTTGTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttatttctaattgttttcaaggttagtatgagttgcatattttttttctcagGCTGGAGGCTACATATTTGAGTTTGACAATGTTGGTAACCGTGACCAATGTCGAGACTTTGTAG
       ttctaat  putative branch site (score: 41)
                                      catattttttttctc  putative PPT
     atttctaattgtttt  TA-rich tract