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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgataacctgtcaaattgtagacaaaacttgattttctgattttttttgtcatttttatttccttatctgttttgtcttgcctctatttcttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAA

Basic information

species Zea mays
transcript GRMZM2G087692_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087692_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g10200.1 (Oryza sativa), 3'ss of exon 4
gtgataacctgtcaaattgtagacaaaacttgattttctgattttttttgtcatttttatttccttatctgttttgtcttgcctctatttcttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAA
||||||||||  |||  | || | | |  ||||  ||     |    |   ||| |     |  |  | ||  ||| | |    |   | || | |||||||| || ||||| || || ||| ||||||||||||| || || || ||||||||||| |||||||| |||||||| |||
gtgataacctagcaagctttaaa-atattttgacatttaccatggcatcagcatatcctaattatcctttgacttgcccttttccggatgctataatcagGGAACTAAGAATAGCTTGTACAATTGCTCAAATGGAGCGTGAGGGTGGCATCAGTCCCCGAATGTCACCTTTAGCACAA
















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|50328095|gb|CO523221.1|CO523221
EST:     CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAA                         GGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT
genomic: CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAAgtgataacct ... cttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT
EST: gi|101393422|gb|EB818643.1|EB818643
EST:     CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAA                         GGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT
genomic: CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAAgtgataacct ... cttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT
EST: gi|89762249|gb|DY689931.1|DY689931
EST:     CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAA                         GGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT
genomic: CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAAgtgataacct ... cttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT
EST: gi|22819976|gb|BU500066.1|BU500066
EST:     CAACCTGATGGCCTTTTTCTGTCAGCAATTCTTGGTGGAGAAACACTGAA                         GGAGCTTAGAATTGCATGCACCA-TTGCTCA
genomic: CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAAgtgataacct ... cttttatcagGGAGCTTAGAATTGCATGCAC-AGTTGCTCA
EST: gi|78078319|gb|DV506734.1|DV506734
EST:     CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAA                         GGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT
genomic: CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAAgtgataacct ... cttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT
EST: gi|74241982|gb|DT649896.1|DT649896
EST:     CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAA                         GGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT
genomic: CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAAgtgataacct ... cttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT
EST: gi|93282992|gb|EB675256.1|EB675256
EST:     CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAA                         GGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT
genomic: CAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAAgtgataacct ... cttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCAT

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: 35 (upstream exon), 42 (downstream exon)
Score: 13

GCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAAgtgataacct ... cttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAA


Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 18

GCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAAgtgataacct ... cttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAA


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 32

GCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAAgtgataacct ... cttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAA


Block sizes: 42 (upstream exon), 27 (downstream exon)
Score: 19

GCTGGCGTTGCAACCTGATGGCCTTTTTCTGGCAGCAATTCTTGGTGGAGAAACACTGAAgtgataacct ... cttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtcatttttatttccttatctgttttgtcttgcctctatttcttttatcagGGAGCTTAGAATTGCATGCACAGTTGCTCAAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAA
              tttccttatctgtttt  CT-rich tract
       atttttatttccttat  TA-rich tract