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

gtcatatgcttgatttgtggttcactaaagttgggttacatatatataggtctggttctgatgttgctcggatgactgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAGAACTTGATTGGAGCATTCTACCAGCCACAATGTGTTCTAATTGACACAG

Basic information

species Zea mays
transcript GRMZM2G573867_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G573867_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g36800.1 (Oryza sativa), 3'ss of exon 3
gtcatatgcttgatttg--tggttcactaaagttgggttacatatatataggt-ctggttctgatgttgctcggatgactgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAGAACTTGATTGGAGCATTCTACCAGCCACAATGTGTTCTAATTGACACAG
||| || |||||||||   |  || |||| | |||| |||||| ||  | | | ||     ||| | |||  | ||   | ||||||||||||||||||||||| ||||| || || |||||||| ||| | ||||||||||| ||||| || |||||||||||||| ||||| || || ||||| |
gtcctaagcttgatttagattttttactacaattgg-ttacatgtagcttgatgctaacggtga-gctgcatgaat---tactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAGAACTTAATTGGGGCGTTCTACCAGCCACAGTGTGTACTGATAGACACCG

upper sequence: GRMZM2G573867_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 3
--------gtcatatgcttgatttgtggttcact---aaagttgggttacatat---atataggtctggttctgatgt--tgctcggatgactgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAGAACTTGATTGGAGCATTCTACCAGCCACAATGTGTTCTAATTGACACAG
          || |  ||   |||    |||  |   ||| ||||     || |   || |  |   | ||||||     |       |   |  | ||||||||||| || ||||| || |||||||| || ||||| || ||||| || || |||||||| || |||||||| || || ||||| || || ||||| |
aaaaaaaaaccaaaaactaactttaatattcttttttaaacttggcacttatgttgaatttcagctggcttctgaaaaaataactattttttttttctagGTGGATTCTTCAGTTGGAGGCAAAACTGGCATAAACCATCCTCTAGGAAAAAATTTGATTGGTGCTTTCTACCAACCTCAGTGTGTACTTATAGACACTG
















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|148956744|gb|EC902625.2|EC902625
EST:     TCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAG                         GTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAG
genomic: TCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAGgtcatatgct ... actgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAG
EST: gi|148946595|gb|EC891854.2|EC891854
EST:     TCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAG                         GTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAG
genomic: TCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAGgtcatatgct ... actgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAG
EST: gi|50336564|gb|CO531690.1|CO531690
EST:     TCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAG                         GTGGATTCATCTGTTGGCGGGA
genomic: TCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAGgtcatatgct ... actgctttagGTGGATTCATCTGTTGGCGGGA
EST: gi|88746263|gb|DY530404.1|DY530404
EST:     TCCTCCGGGGCGTCAATTTCATACAGATACCATCTACTCAGATGGCCCAG                         GTGGATTCATC
genomic: TCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAGgtcatatgct ... actgctttagGTGGATTCATC
EST: gi|78082241|gb|DV510653.1|DV510653
EST:     TCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAG                         GTGGATTCATCTGTTGGCGGGGAAAACTGGGATTAACCACCCACT
genomic: TCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAGgtcatatgct ... actgctttagGTGGATTCATCTGTTGGCGGG-AAAACTGGGATTAACCACCCACT
EST: gi|149043950|gb|EE047432.2|EE047432
EST:     TCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAG                         GTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAG
genomic: TCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAGgtcatatgct ... actgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAG

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: 43 (upstream exon), 47 (downstream exon)
Score: 31

ACTGGGTGGTGGTGTCATCGGGGACATGTGTGGATTTGCAGCTGCTGCATTCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAGgtcatatgct ... actgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAGAACTTGATTGGAGCATTCTACCAGCCACAATGTGTTCTAATTGACACAG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 64

ACTGGGTGGTGGTGTCATCGGGGACATGTGTGGATTTGCAGCTGCTGCATTCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAGgtcatatgct ... actgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAGAACTTGATTGGAGCATTCTACCAGCCACAATGTGTTCTAATTGACACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 143

ACTGGGTGGTGGTGTCATCGGGGACATGTGTGGATTTGCAGCTGCTGCATTCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAGgtcatatgct ... actgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAGAACTTGATTGGAGCATTCTACCAGCCACAATGTGTTCTAATTGACACAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 87

ACTGGGTGGTGGTGTCATCGGGGACATGTGTGGATTTGCAGCTGCTGCATTCCTCCGGGGCGTCAATTTCATACAGATACCAACTACTCTGATGGCCCAGgtcatatgct ... actgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAGAACTTGATTGGAGCATTCTACCAGCCACAATGTGTTCTAATTGACACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgggttacatatatataggtctggttctgatgttgctcggatgactgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAGAACTTGATTGGAGCATTCTACCAGCCACAATGTGTTCTAATTGACACAG
                          ttctgat  putative branch site (score: 87)
                                              ctgcttt  putative PPT
      ttacatatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatatgcttgatttgtggttcactaaagttgggttacatatatataggtctggttctgatgttgctcggatgactgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAGAACTTGATTGGAGCATTCTACCAGCCACAATGTGTTCTAATTGACACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA