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

gtcaagatcttcctgtcatattggagaacattttaagtttttaacataataatctctttggtctgatttaatcatatgcccaggttcagattcttacaatatatctatttgtgacagGACCTGATTTTGATGAGGCAAAACAATATCAATGCTGTTAGAAATAGCCATTACCCACAGCACCCAAGGTGGTATGAGTTATGTGACATTTTTGGTCTTT

Basic information

species Zea mays
transcript GRMZM2G032496_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 9
gtcaagatcttcctgtcatattggagaacattttaag-tttttaacataataatctctttggtctgatttaatcatatgcccagg-----ttcagattcttacaatatatctatttgtgacagGACCTGATTTTGATGAGGCAAAACAATATCAATGCTGTTAGAAATAGCCATTACCCACAGCACCCAAGGTGGTATGAGTTATGTGACATTTTTGGTCTTT
   |      | |||||| | ||    | || | |||   |||   || |  ||||||||||   | |||  |  |   ||||||     ||||| |  | || || ||| |||||||||||||| ||| |||||||||| |||||||| || |||||||||||||| |||||||| || || || ||||||||||||||| | |||||||||||||| ||||
-gtagctctcttctgtca-actgtc--atatctgaagacatttcgtattactatctctttggctcgtttt--tttttctcccaggctgttttcaggtattaactatttatttatttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT

upper sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G26700.1 (Glycine max), 3'ss of exon 8
gtcaagatcttcctgtcatattggagaacattttaagtttttaacataataatctctttggtctgatttaatcatatgcccaggttcagattcttacaatatatctatttg------tgacagGACCTGATTTTGATGAGGCAAAACAATATCAATGCTGTTAGAAATAGCCATTACCCACAGCACCCAAGGTGGTATGAGTTATGTGACATTTTTGGTCTTT
                  || ||   | | ||||      || | |||| ||  |  || || |    |   || ||||     ||    || |||  | |    || |||      | ||||||  || | || |||| |||||||||||| |||||||| || || |||||||| || || || ||| | ||||||||| |||||||  | |||||  | |
-----------------gtactgctaatctttttttccccttca-ataa-aaaattgttagtttatgatggccaaatgct---atttgtttttttaagacactaataattgctgtgcttacagGATTTGGTCTTAATGAAGCAAAACAATATTAATGCTGTGAGGAACAGCCATTATCCCCAACATCCACGTTGGTATGAGCTATGTGATTTGTTTGGCATGT

upper sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv13s0067g03000.t01 (Vitis vinifera), 3'ss of exon 8
gt-caagatcttcctgtcata----ttggagaacattttaagtttttaacataataatctctttggtctgatttaatcatatgcccaggttcagattcttacaatatatctatttgtgacagGACCTGATTTTGATGAGGCAAAACAATATCAATGCTGTTAGAAATAGCCATTACCCACAGCACCCAAGGTGGTATGAGTTATGTGACATTTTTGGTCTTT
|| |||  || || |||  |     ||||| | ||| ||    | ||||  ||||       ||||| |||||  |||||||      ||  ||||  | |  |    ||| |     ||||||  || || | |||| ||||||||||||||||||||| ||||| |||||||| || || || ||  | ||||| ||||| |||||  | |||||  | |
gtgcaacctcctcttgttgttctctttggatatcatctttgtgtgttaagttaatg------ttggtttgatt-gatcatatt-----gtcgagatcttcattac---tctctggcatacagGATTTGGTTCTAATGAAGCAAAACAATATCAATGCTGTGAGAAACAGCCATTATCCCCAACATCCTCGATGGTACGAGTTGTGTGATTTGTTTGGCATGT

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: 45 (upstream exon), 49 (downstream exon)
Score: 35

AATGCTCGTCAATGGATGTCCTGTTGTGCTAAGAGGTGTCAACAGACATGAGCACCATCCACGCCTTGGAAAGACAAATTTAGAAGCATGCATGATCAAGgtcaagatct ... tttgtgacagGACCTGATTTTGATGAGGCAAAACAATATCAATGCTGTTAGAAATAGCCATTACCCACAGCACCCAAGGTGGTATGAGTTATGTGACATTTTTGGTCTTT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 45

AATGCTCGTCAATGGATGTCCTGTTGTGCTAAGAGGTGTCAACAGACATGAGCACCATCCACGCCTTGGAAAGACAAATTTAGAAGCATGCATGATCAAGgtcaagatct ... tttgtgacagGACCTGATTTTGATGAGGCAAAACAATATCAATGCTGTTAGAAATAGCCATTACCCACAGCACCCAAGGTGGTATGAGTTATGTGACATTTTTGGTCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 45

AATGCTCGTCAATGGATGTCCTGTTGTGCTAAGAGGTGTCAACAGACATGAGCACCATCCACGCCTTGGAAAGACAAATTTAGAAGCATGCATGATCAAGgtcaagatct ... tttgtgacagGACCTGATTTTGATGAGGCAAAACAATATCAATGCTGTTAGAAATAGCCATTACCCACAGCACCCAAGGTGGTATGAGTTATGTGACATTTTTGGTCTTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 44

AATGCTCGTCAATGGATGTCCTGTTGTGCTAAGAGGTGTCAACAGACATGAGCACCATCCACGCCTTGGAAAGACAAATTTAGAAGCATGCATGATCAAGgtcaagatct ... tttgtgacagGACCTGATTTTGATGAGGCAAAACAATATCAATGCTGTTAGAAATAGCCATTACCCACAGCACCCAAGGTGGTATGAGTTATGTGACATTTTTGGTCTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatttaatcatatgcccaggttcagattcttacaatatatctatttgtgacagGACCTGATTTTGATGAGGCAAAACAATATCAATGCTGTTAGAAATAGCCATTACCCACAGCACCCAAGGTGGTATGAGTTATGTGACATTTTTGGTCTTT
                            ttcttac  putative branch site (score: 44)
                                         tctattt  putative PPT
                           attcttacaatatatc  TA-rich tract