Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAGgttctattataaatatccatttgaacagtccattagttcataagaatcaatatgactcttactataaacttttcggtcttcctttgcag

Basic information

species Zea mays
transcript GRMZM2G016561_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016561_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g74330.1 (Oryza sativa), 5'ss of exon 7
TGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAGgttctattataaatatccatttgaacagtcca--ttagttcataagaatcaatatgactcttactataaacttttcggtcttcctttgcag
||||| |||||||||||||| || ||| ||||||||||||| |||||||| ||||||||||||||||||||||||||||| | |||||   ||||  || | |   ||||  ||   | |  ||   |||||| | | | |  | ||| || | |    |||||| |||
TGCTTTTTCCCACAAGAAGTGGCGAAAGGCATCACCACCCCAATGTTTATTCTCAATCCAGCATATGATGTTTGGCAGgtaccattatccgtatctgttggcaggttccatgttctgttagcagctccaatattagtgtgataaaaaatttgttg----tccttttcag
















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|149085716|gb|EE175235.2|EE175235
EST:     GCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAG                         GTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAA
genomic: GCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAGgttctattat ... tcctttgcagGTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAA
EST: gi|78112623|gb|DV531017.1|DV531017
EST:     GCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAG                         GTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAA
genomic: GCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAGgttctattat ... tcctttgcagGTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAA
EST: gi|71771147|gb|DR969084.1|DR969084
EST:     GCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAG                         GTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAA
genomic: GCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAGgttctattat ... tcctttgcagGTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAA
EST: gi|71426622|gb|DR807672.1|DR807672
EST:     GCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAG                         GTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAA
genomic: GCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAGgttctattat ... tcctttgcagGTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAA

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: 82

TGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAGgttctattat ... tcctttgcagGTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAAAATTGCAGGATGGATATTAGCAGGTGTAGCTCAAAACAGCTTGAAGTTC


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 37

TGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAGgttctattat ... tcctttgcagGTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAAAATTGCAGGATGGATATTAGCAGGTGTAGCTCAAAACAGCTTGAAGTTC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 46

TGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAGgttctattat ... tcctttgcagGTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAAAATTGCAGGATGGATATTAGCAGGTGTAGCTCAAAACAGCTTGAAGTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

TGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAGgttctattat ... tcctttgcagGTAGAGCATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAAAATTGCAGGATGGATATTAGCAGGTGTAGCTCAAAACAGCTTGAAGTTC