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

gtacgaatctgtgggacaattgtaaatcccattacatatatttagttccccatttgtttttgttgcaactgtgcgtaatatttggatacactctttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCCTTCATAGAGTTCACTGATGAGG

Basic information

species Zea mays
transcript GRMZM2G173428_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
gtacgaatctgtgggacaattgtaaatcccattacatatatttagttccccatttg-tttttgttgcaactgtgcgtaata--tttgga--tacactctttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCCTTCATAGAGTTCACTGATGAGG
                                ||||| | | | | ||| || ||| ||| |||   || ||||| |||||   ||| |  |   || | ||||||||||||||||||| |||||||| || || || || || ||||| || || ||||||||||||||||||||||
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
gtacgaatctgtgggacaattgtaaatcccattacatatatttagttccccatttgtttttgttgcaactgtgcgtaatatttggatacactctttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCCTTCATAGAGTTCACTGATGAGG
       |       |   |  | || | | | |  |||    |  |||    ||||  ||| |     |||| ||  || | |  |    | ||   ||||||| ||||||||||| || || ||||||||||| ||||||||||| || |||||||||||||||||||| |
------gttgaaaatattttcttgaagctc-tcatctatg---aactccatcattgtgcttggt-----tgtgtgtcttact-gtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
















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|9743159|gb|BE519307.1|BE519307
EST:     CAGGTTACTGAAGAAAACCTGGCAGCACTATTTATAAATTGTGGACAG                         GTTGTGGACTGTGCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGC
genomic: CAGGTTACTGAAGAAAACCTGGCAGCACTATTTATAAATTGTGGACAGgtacgaatct ... ctctttgaagGTTGTGGACTGT-CGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGC
EST: gi|78116430|gb|DV534817.1|DV534817
EST:     GTTACTGAAGAAAACCTGGCAGCACTATTTATAAATTGTGGACAG                         GTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCC
genomic: GTTACTGAAGAAAACCTGGCAGCACTATTTATAAATTGTGGACAGgtacgaatct ... ctctttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCC

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: 49 (upstream exon), 48 (downstream exon)
Score: 128

GTTACTGAAGAAAACCTGGCAGCACTATTTATAAATTGTGGACAGgtacgaatct ... ctctttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCCTTCATAGAGTTCACTGATGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 264

GTTACTGAAGAAAACCTGGCAGCACTATTTATAAATTGTGGACAGgtacgaatct ... ctctttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCCTTCATAGAGTTCACTGATGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

GTTACTGAAGAAAACCTGGCAGCACTATTTATAAATTGTGGACAGgtacgaatct ... ctctttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCCTTCATAGAGTTCACTGATGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 217

GTTACTGAAGAAAACCTGGCAGCACTATTTATAAATTGTGGACAGgtacgaatct ... ctctttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCCTTCATAGAGTTCACTGATGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccccatttgtttttgttgcaactgtgcgtaatatttggatacactctttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCCTTCATAGAGTTCACTGATGAGG
                                           cactcttt  CT-rich tract
      atttgttttt  TA-rich tract