Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcttgatgcttgatattggctcttaattttatgcttcagtaatgccatcagcttattgcctttcttattgctgataacacacttcaccactggtttagGCTCTTGTTGAAAAGGATTGGTTAGCATTTGGTCATCCATTTGCAGAGAGAATGGGAGTTCCAACAGTATCTGAGAATGGGGGGTCACAGTATGAGCTAC

Basic information

species Zea mays
transcript GRMZM2G046050_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046050_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g44260.1 (Oryza sativa), 3'ss of exon 14
---gtgcttgatgcttgatattggctcttaattttatgcttcagtaatgccatcagcttattgcctttcttattgctgataacacacttcac--cactggtttagGCTCTTGTTGAAAAGGATTGGTTAGCATTTGGTCATCCATTTGCAGAGAGAATGGGAGTTCCAACAGTATCTGAGAAT---GGGGGGTCACAGTATGAGCTAC
   ||  |   |||| |   ||   |   ||  |  | ||||| |||  | ||  |  | ||  | || |   |     |||| | || |||  ||||  ||||||| ||||| |||||||||||| |||||||||| ||||||||||||||| ||||||||||||||||  || |||| |||    | || ||||||| |||||   
tacgttttaagtgctgg---tttatttcaaacatgttacttcaataacacaattggaattttcacattttggatat--gtaaccctctgcactacacttctttagGCCCTTGTGGAAAAGGATTGGCTAGCATTTGGCCATCCATTTGCAGAGCGAATGGGAGTTCCAACGATAACTGATAATAATAGTGGATCACAGTTTGAGC---

upper sequence: GRMZM2G046050_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 14
gtgcttgatgcttgatattggctcttaattttatgcttcagtaatgccatcagct----tattgcctttcttattgctgataacacacttcaccactggtttagGCTCTTGTTGAAAAGGATTGGTTAGCATTTGGTCATCCATTTGCAGAGAGAATGGGAGTTCCAACAGTATCTGAGAATGGGGGGTCACAGT-ATGAGCTAC
   ||||     ||||       | |||        |  |  | |    |  | |     |||| |||   || |  |    ||    |    |      | |||||||||| ||||||||||||||| |||||||||| |||||| | ||  |  ||||| | ||||  || |||||   |||    |   | | |  |  |  
---cttgccagctgattcaactgcataagcagcccttataagatttttgtttgatgcaccattgtcttatgtagtctttcctac-tgttctgacttcacatcagGCTCTTGTCGAAAAGGATTGGTTATCATTTGGTCACCCATTTTCGGATCGGGTGGGAATGCCAAACGTGTCTGAATCTGGTAATTTTGAATTACCAATTC-

upper sequence: GRMZM2G046050_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0074g00300.t01 (Vitis vinifera), 3'ss of exon 14
---gtgcttgatgcttgatattggctcttaattttat-gcttcagtaatgcc-atcagcttattgcctttcttattgctgataacacacttcaccactggtttagGCTCTTGTTGAAAAGGATTGGTTAGCATTTGGTCATCCATTTGCAGAGAGAATGGGAGTTCCAACAGTATCTGAGAATGGGGGGTCACAGTATGAGCTAC
        |||       | |     ||  || | ||  |||||      |  ||  |  |||  ||||| |  ||     |||     || |    |  | ||||| ||||||||||| || ||| | |||||||||||||||||| ||||  | |||||  | ||||| |||||||  | ||        |  | |||  || 
atctaagctgacatgaagtgtccttactgcatatgattacttcacaggcacttatttggatatcacctttatattt-----taaagtgttttatttttcatgtagGCACTTGTTGAAAAAGACTGGCTTGCATTTGGTCATCCATTTTCAGATCGCATGGGGATGCCAACTGTATCTGGAAGTGTTAACATGCCCTTTGAATTAT

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: 47 (upstream exon), 46 (downstream exon)
Score: 19

TGATGGATGGGACCGCACAACCCAGTTGGTTTCACTTGCTTGTTTATTGCTTGATCCCTATTATCGAACTTTCAGTGGATTCCAGgtaaacagtt ... actggtttagGCTCTTGTTGAAAAGGATTGGTTAGCATTTGGTCATCCATTTGCAGAGAGAATGGGAGTTCCAACAGTATCTGAGAATGGGGGGTCACAGTATGAGCTAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 24

TGATGGATGGGACCGCACAACCCAGTTGGTTTCACTTGCTTGTTTATTGCTTGATCCCTATTATCGAACTTTCAGTGGATTCCAGgtaaacagtt ... actggtttagGCTCTTGTTGAAAAGGATTGGTTAGCATTTGGTCATCCATTTGCAGAGAGAATGGGAGTTCCAACAGTATCTGAGAATGGGGGGTCACAGTATGAGCTAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 29

TGATGGATGGGACCGCACAACCCAGTTGGTTTCACTTGCTTGTTTATTGCTTGATCCCTATTATCGAACTTTCAGTGGATTCCAGgtaaacagtt ... actggtttagGCTCTTGTTGAAAAGGATTGGTTAGCATTTGGTCATCCATTTGCAGAGAGAATGGGAGTTCCAACAGTATCTGAGAATGGGGGGTCACAGTATGAGCTAC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 54

TGATGGATGGGACCGCACAACCCAGTTGGTTTCACTTGCTTGTTTATTGCTTGATCCCTATTATCGAACTTTCAGTGGATTCCAGgtaaacagtt ... actggtttagGCTCTTGTTGAAAAGGATTGGTTAGCATTTGGTCATCCATTTGCAGAGAGAATGGGAGTTCCAACAGTATCTGAGAATGGGGGGTCACAGTATGAGCTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatcagcttattgcctttcttattgctgataacacacttcaccactggtttagGCTCTTGTTGAAAAGGATTGGTTAGCATTTGGTCATCCATTTGCAGAGAGAATGGGAGTTCCAACAGTATCTGAGAATGGGGGGTCACAGTATGAGCTAC
                            tgataac  putative branch site (score: 54)
                 tttcttatt  TA-rich tract