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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtacacctatccatccagtttcagcgacagttatgcactttatgtttgatgttatataacctgattataacaaatatgttatgactgtctctatgtagAATGTGCCACCTGCCCTACTAGTACGATTTCTGAGGGAGCATCGCTCCGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCCGCTGCTCTTAGGGCTA

Basic information

species Zea mays
transcript GRMZM2G423337_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g43930.1 (Oryza sativa), 3'ss of exon 11
gtctgtacacctatccatccagtttcagcgacagttatgcactttatgtttgatgttatataacctgattataacaaatatgttatgactgtctctatgtagAATGTGCCACCTGCCCTACTAGTACGATTTCTGAGGGAGCATCGCTCCGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCCGCTGCTCTTAGGGCTA
|||| ||| | ||   ||||| | |  |  |   || |||| |   |  |||| ||| | ||   |||   | ||||   |||| | | |||      ||||||||| |||||||| || ||||| |||||| |||||||||| ||||| ||||||||||||||||||||||||||||||||||| |||||  | |||||||
gtctttactcata---atcca-tctaggtaattattgtgca-tgagtagttga-gttgtttattatgacc-tgacaagcttgttttcattgt------gtagAATGTACCACCTGCTCTCCTAGTGCGATTTTTGAGGGAGCACCGCTCTGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCTGCTGCGTTGAGGGCTA
















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), 49 (downstream exon)
Score: 732

TTCTCCAAACAAACTTATTGGTCCTCATGTCAACTCTTCCCAGCTGTTTACTGCGATCGGAGGTGGCATCCTGTGTGCTAAGGCATCAATGCTGCTTCAGgtctgtacac ... ctctatgtagAATGTGCCACCTGCCCTACTAGTACGATTTCTGAGGGAGCATCGCTCCGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCCGCTGCTCTTAGGGCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

TTCTCCAAACAAACTTATTGGTCCTCATGTCAACTCTTCCCAGCTGTTTACTGCGATCGGAGGTGGCATCCTGTGTGCTAAGGCATCAATGCTGCTTCAGgtctgtacac ... ctctatgtagAATGTGCCACCTGCCCTACTAGTACGATTTCTGAGGGAGCATCGCTCCGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCCGCTGCTCTTAGGGCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 316

TTCTCCAAACAAACTTATTGGTCCTCATGTCAACTCTTCCCAGCTGTTTACTGCGATCGGAGGTGGCATCCTGTGTGCTAAGGCATCAATGCTGCTTCAGgtctgtacac ... ctctatgtagAATGTGCCACCTGCCCTACTAGTACGATTTCTGAGGGAGCATCGCTCCGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCCGCTGCTCTTAGGGCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

TTCTCCAAACAAACTTATTGGTCCTCATGTCAACTCTTCCCAGCTGTTTACTGCGATCGGAGGTGGCATCCTGTGTGCTAAGGCATCAATGCTGCTTCAGgtctgtacac ... ctctatgtagAATGTGCCACCTGCCCTACTAGTACGATTTCTGAGGGAGCATCGCTCCGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCCGCTGCTCTTAGGGCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgatgttatataacctgattataacaaatatgttatgactgtctctatgtagAATGTGCCACCTGCCCTACTAGTACGATTTCTGAGGGAGCATCGCTCCGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCCGCTGCTCTTAGGGCTA
                     ttataac  putative branch site (score: 98)
                                         ctgtctct  putative PPT
                  tgattataacaaatat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtacacctatccatccagtttcagcgacagttatgcactttatgtttgatgttatataacctgattataacaaatatgttatgactgtctctatgtagAATGTGCCACCTGCCCTACTAGTACGATTTCTGAGGGAGCATCGCTCCGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCCGCTGCTCTTAGGGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT