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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGCATGTGGGACAGTTATCCGATGTTTCCCACTAGATTAAAGAAATTTGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAGgtattgtttttattaatatatcacttacctgacatataaacatttatataacagcaactactgattgcag

Basic information

species Zea mays
transcript GRMZM2G101250_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101250_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os04g09860.3 (Oryza sativa), 5'ss of exon 15
TTTGGCATGTGGGACAGTTATCCGATGTTTCCCACTAGATTAAAGAAATTTGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAGgtattgttttta-------ttaatatatcacttacctgacatataaacatttatataacagcaactactgattgcag
|| || |||||||||| |||||||||||||||||| |||||||| || ||||||||||| || || ||||| |||||| |||||||| | ||||| ||||||| ||| ||||       ||| ||| |  ||  ||| |  |  |||| ||| ||      || || ||||   |||
TTCGGTATGTGGGACAATTATCCGATGTTTCCCACCAGATTAAAAAAGTTTGATAACATCGGTCTTGTAGAAGCCATTGTTAGTAGTATCCTTTCGACAGgtagtgtctttactcttccttattattttgctccccttatcttgaaacttttcta-----acacctgctgaccacag
















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|60358881|gb|DN225854.1|DN225854
EST:     TGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAG                         GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
genomic: TGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
EST: gi|148934268|gb|EC878291.2|EC878291
EST:     TGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAG                         GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
genomic: TGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
EST: gi|78121627|gb|DV540011.1|DV540011
EST:     TGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAG                         GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
genomic: TGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
EST: gi|40302924|gb|CK347311.1|CK347311
EST:     T-ATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAG                         GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
genomic: TGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
EST: gi|60358880|gb|DN225853.1|DN225853
EST:     TGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAG                         GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
genomic: TGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
EST: gi|32834623|gb|CD974301.1|CD974301
EST:     ACTTTCAACAG                         GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
genomic: ACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
EST: gi|32930313|gb|CF035125.1|CF035125
EST:     ACTTTCAACAG                         GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
genomic: ACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
EST: gi|32833197|gb|CD972875.1|CD972875
EST:     GTACTTTCAACAG                         GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
genomic: GTACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
EST: gi|91056340|gb|EB166758.1|EB166758
EST:     TGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAG                         GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG
genomic: TGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 30

TTTGGCATGTGGGACAGTTATCCGATGTTTCCCACTAGATTAAAGAAATTTGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 1

TTTGGCATGTGGGACAGTTATCCGATGTTTCCCACTAGATTAAAGAAATTTGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG


Block sizes: 49 (upstream exon), 27 (downstream exon)
Score: 7

TTTGGCATGTGGGACAGTTATCCGATGTTTCCCACTAGATTAAAGAAATTTGATAACATTGGCCTCGTAGAGGCCATTATTAGTAGTGTACTTTCAACAGgtattgtttt ... ctgattgcagGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG