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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTACAGACTTGTCGTTCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcacattctctaattttccttttattttcactagctaggcaggaatttatgtttgaaaattggcaacttgcagtgtttgataatgttagactac...

Basic information

species Zea mays
transcript GRMZM2G702159_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G702159_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 5'ss of exon 5
ATTACAGACTTGTCGTTCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcacattctctaattttccttttattttcactagctaggcaggaatttatgtttgaaaattggcaacttgcagtgtttg-ataatgttagactac--------------------------------------------------------------------------
|| ||||||||  | |||||| |||||||||| |||||||| || |||  ||||||||||||||||||  |||    ||||| | |||  |   |     || |   ||   | |  || |  ||||||   ||   || ||||   || |   | |   | | ||                                                                           
ATCACAGACTTACCATTCTCTCTTTATTCAACATTTGTTATTGAAGCTAAACATGGTTTTAACAAGgtatgtttgtgttctcaattttagcacct-----cagttatta--tatgttttaacatttgaatggtgttcacctgcaagattagtgaagtacaaaagtatcttggcttatgaatttgctatgttctaatccccaacatatttattctgaacctctagctttggacttttttcag

upper sequence: GRMZM2G702159_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G47190.1 (Glycine max), 5'ss of exon 5
ATTACAGACTTGTCGTTCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcacattctctaattttccttttattttcactagctaggcaggaatttatgtttgaaaattggcaacttg---cagtgtttgataatgttagactac
 | || || ||| | || ||| | || ||||||||||| || ||||| || ||||||||||||||||| |||   | | ||  || ||      |   |  | ||  |         ||| |  || |    |   |  |||       || | ||  ||| | | |  
-TAACTGATTTGCCCTTTTCTCTGTACTCAACTTTTGTGATTGAGGCCCGTCATGGTTTTAACAAGGttcgtattcttccttcaaattcaaccatccatctattatttcattcatg-tttttagttcactccttttattttgatttgacgtctcattttgtaatattg-
















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|40286942|gb|CK327334.1|CK327334
EST:     CTCTATTTATTCAACTTTTGGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATCAGGGATATGATCAANGGAGTTTTACTATTC
genomic: CTCTATTTATTCAACTTTTG-TTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcac ... tcccttgtagCAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTC
EST: gi|40286924|gb|CK327316.1|CK327316
EST:     TCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcac ... tcccttgtagCAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTC
EST: gi|91875692|gb|EB405649.1|EB405649
EST:     TCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTC
genomic: TCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcac ... tcccttgtagCAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTC
EST: gi|34391316|gb|CF384544.1|CF384544
EST:     TCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTC
genomic: TCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcac ... tcccttgtagCAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTC
EST: gi|101394395|gb|EB819132.1|EB819132
EST:     TCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTC
genomic: TCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcac ... tcccttgtagCAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTC

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: 45 (upstream exon), 43 (downstream exon)
Score: 28

ATTACAGACTTGTCGTTCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcac ... tcccttgtagCAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTCATGATACTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG


Block sizes: 31 (upstream exon), 40 (downstream exon)
Score: 3

ATTACAGACTTGTCGTTCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcac ... tcccttgtagCAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTCATGATACTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG


Block sizes: 40 (upstream exon), 43 (downstream exon)
Score: 12

ATTACAGACTTGTCGTTCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcac ... tcccttgtagCAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTCATGATACTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG


Block sizes: 41 (upstream exon), 41 (downstream exon)
Score: 16

ATTACAGACTTGTCGTTCTCTATTTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgcgttcac ... tcccttgtagCAAACTATATGGCTCTTCATCAGGGATATGATCAAAGGAGTTTTACTATTCATGATACTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG