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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatttctctccacgaacacttgtgtttggaatcactattcaatattttctaatattgcattgtcattccagAGGATTTCAGATCTGTGCAAAAACGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA

Basic information

species Zea mays
transcript GRMZM2G029135_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029135_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g08270.1 (Oryza sativa), 3'ss of exon 7
-------------gtcattt-ctctccacgaacacttgtgtttggaatcactattcaatattttctaatattgcattgtcattccagAGGATTTCAGATCTGTGCAAAAACGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA
              |||||  |  | |||| |||||||  || |   | ||| || | |||||  ||||||||||   |  |||||||| |||||||| ||||||| ||| ||||||||||||||||| |||||||||||||||||
gtaacctgtctctctcattcacagttcacgcacacttgcattcgaggtgact-ttaattatttcttaatattgcaccattgttccagAGAATTTCAGAACTGTGCAGAAATGCTGGTGCATGGCTTGTAGTTGACAATACCTATGA

upper sequence: GRMZM2G029135_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g08270.4 (Oryza sativa), 3'ss of exon 7
-------------gtcattt-ctctccacgaacacttgtgtttggaatcactattcaatattttctaatattgcattgtcattccagAGGATTTCAGATCTGTGCAAAAACGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA-----------------------------------------
              |||||  |  | |||| |||||||  || |   | ||| || | |||||  ||||||||||   |  |||||||| |||||||| ||||||| ||| ||||||||||||||||| |||||||||||||||||                                         
gtaacctgtctctctcattcacagttcacgcacacttgcattcgaggtgact-ttaattatttcttaatattgcaccattgttccagAGAATTTCAGAACTGTGCAGAAATGCTGGTGCATGGCTTGTAGTTGACAATACCTATGAGTAAGTTAGTACTCAATTACTGATTATTGCTCAACTGCAAC
















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|211043538|gb|FL214488.1|FL214488
EST:     TGAATCCGGGGAACCCCTCTGGAGYTTTTATTCCCAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAACGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGTAACCCCTCTGGAGCTTTTATTCCCAGGCCTATGCTTGAGgtcatttctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAACGCTGGTGCATGGCTTGTGGTTGACAAT




















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: 48 (upstream exon), 39 (downstream exon)
Score: 21

GGAGAAGGTTCTGAAAGAAAATGACCCTATCCCTAAACTTGTTACCGTTGTGAATCCGGGTAACCCCTCTGGAGCTTTTATTCCCAGGCCTATGCTTGAGgtcatttctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAACGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 41

GGAGAAGGTTCTGAAAGAAAATGACCCTATCCCTAAACTTGTTACCGTTGTGAATCCGGGTAACCCCTCTGGAGCTTTTATTCCCAGGCCTATGCTTGAGgtcatttctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAACGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

GGAGAAGGTTCTGAAAGAAAATGACCCTATCCCTAAACTTGTTACCGTTGTGAATCCGGGTAACCCCTCTGGAGCTTTTATTCCCAGGCCTATGCTTGAGgtcatttctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAACGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

GGAGAAGGTTCTGAAAGAAAATGACCCTATCCCTAAACTTGTTACCGTTGTGAATCCGGGTAACCCCTCTGGAGCTTTTATTCCCAGGCCTATGCTTGAGgtcatttctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAACGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttgtgtttggaatcactattcaatattttctaatattgcattgtcattccagAGGATTTCAGATCTGTGCAAAAACGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA
                              ttctaat  putative branch site (score: 57)
                                              tcattcc  putative PPT
             aatcactattcaatat  TA-rich tract