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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatactattgaagctattgctgttaatatgcaggtgtgaacacaaggtatcttttctgcttgctgcatgggtgaattgctagtttgtgctaaacta...

Basic information

species Zea mays
transcript GRMZM5G880102_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G880102_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 5'ss of exon 13
GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatactattgaagctattgctgttaatatgcaggtgtgaacacaaggtatcttttctgcttgctgcatgggtgaattgc---tagtttgtgctaaacta
|||||| ||| |||||| ||||| |||||||||||||| || |||||||| ||||||||||| ||||||||||||||||  |  ||||||   ||||   | |||  |   || |     |  ||||    |  |||   |  ||   ||||   |  |    |  ||||| 
GTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCTCGCAGAATTGATAATCAGgtaatatactgattgagctatcattgtttgcaagcaaattgcaagattc--tgcctttgacacaagctctttccgtattttgcatatgatcatggtcaaact-

upper sequence: GRMZM5G880102_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G01060.2 (Glycine max), 5'ss of exon 15
GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatactattgaagctattgctgttaatat--gcaggtgtgaacacaaggtatcttttctgcttgctgcatgggtgaattgctagtttgtgctaaacta
||  |   ||  ||||| || || |||||||| |||||||| |||||||||||  ||||||| ||||||||  | |  |||     || || ||  ||   |    ||||| |||  |  | | |  |  ||  | ||        |  |    |    |   ||   |||
GTTGTGGAAGCTGGTGGACTACATGTAGTAGGCACAGAGCGTCATGAATCACGTCGAATTGATAATCAGgt--ttttttatctttccttttccttgtagggttgaaaggtgggaagccgggatgtaatggcttgtggccttggacatccacatatctcctaccctcttcta

upper sequence: GRMZM5G880102_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G01060.1 (Glycine max), 5'ss of exon 15
GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatactattgaagctattgctgttaatat--gcaggtgtgaacacaaggtatcttttctgcttgctgcatgggtgaattgctagtttgtgctaaacta------------------------------------------------------------------------------------------------
||  |   ||  ||||| || || |||||||| |||||||| |||||||||||  ||||||| ||||||||  | |  |||     || || ||  ||   |    ||||| |||  |  | | |  |  ||  | ||        |  |    |    |   ||   |||                                                                                                
GTTGTGGAAGCTGGTGGACTACATGTAGTAGGCACAGAGCGTCATGAATCACGTCGAATTGATAATCAGgt--ttttttatctttccttttccttgtagggttgaaaggtgggaagccgggatgtaatggcttgtggccttggacatccacatatctcctaccctcttctattattcttgcagctataatagctactgctacttctaccactcctaccctgtcaaataagtatttaaagttggaactttttttcatcatccataaag

upper sequence: GRMZM5G880102_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G27810.1 (Glycine max), 5'ss of exon 15
GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatactattgaagctattgctgttaatatgcaggtgtgaacacaaggtatcttttctgcttgctgcatgggtgaattgc-tagtttgtgctaaacta----------------------------------------------------------------------------------------------------
||  |   ||  || || || || |||||||| |||||||| |||||||||||  ||||||| ||||||||  | |  | ||    || || ||  |||  |  |   | |   |   || || |  |  |||||  || | ||  |  ||| ||  |  | |     |                                                                                                     
GTTGTGGAAGCTGGCGGACTACATGTAGTAGGCACAGAGCGTCATGAATCACGTCGAATTGATAATCAGgttttctcttctttc--cttttccttgtaaggttgaaaggagggaaactgggatgtactg-gcttgtggccttggacatctgcatatctcctaccctcttctattattattgcagctataataactactgctgcttctaccactcctaccctgttaaataagtatttaaaattggaacatttttttttatcatccataaag

upper sequence: GRMZM5G880102_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 14
GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatactattgaagctattgctgttaatatgcaggtgtgaacacaaggtatcttttctgcttgctgcatgggtgaattgctagtttgtgctaaacta------
||  |   ||  ||||| |||||||| || || |||||||| |||||||||||  |||| |||||||||||  |    || |  |  | ||       | ||  | |  |||     |||| || |||||   ||    |    |   |  |||  || || |   ||       
GTGGTGGAAGCTGGTGGACTTCACGTGGTGGGGACAGAGCGGCATGAATCACGTCGAATAGACAATCAGgt--ttccttaatagatttgtt-tcaaggagatttatggttgattc--aggt-tcctttctcagtgaaataaatcttcttcactatgttttgttcccctcatacag

upper sequence: GRMZM5G880102_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ15249 (Selaginella moellendorffii), 5'ss of exon 14
GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatactattgaa-gctattgctgttaatatgcaggtgtgaacacaaggtatcttttctgcttgctgcatgggtgaattgctagtttgtgctaaacta
||  || | | |||||| ||||||||  |||| |||||||||||||||||||| |||||||| |||||||||   ||   ||| | | | |   | | |     ||    |    |||                                                    
GTTGTTGCTGCAGGTGGCCTTCACGTGATAGGCACAGAGCGCCATGAATCACGAAGAATTGATAATCAGgtatagtaaccttggatgttctctgtataacgccccatcctttgttacag---------------------------------------------------

upper sequence: GRMZM5G880102_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ08380 (Selaginella moellendorffii), 5'ss of exon 14
GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatactattgaagctattgctgttaatatgc-aggtgtgaacacaaggtatcttttctgcttgctgcatgggtgaattgctagtttgtgctaaacta
||  || | | |||||| ||||||||  |||| ||||||||||| |||||||| |||||||| |||||||||   ||   ||  |  |  |     |||    | |    |    |||                                                    
GTTGTTGCTGCAGGTGGCCTTCACGTGATAGGCACAGAGCGCCACGAATCACGAAGAATTGATAATCAGgtatagtaaccttagatgttctctgcataacgccccatcctttgttacag---------------------------------------------------

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|226431424|gb|GO477760.1|GO477760
EST:     TTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG                         CTCCGTGGTCGAAGTGGAAGACAGGGGGATCCTGGAAGCTCTCGCTTCTTT
genomic: TTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatact ... tctggtttagCTCCGTGGTCGAAGTGGAAGACAGGGGGATCCTGGAAGCTCTCGCTTCTTT




















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), 45 (downstream exon)
Score: 78

GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatact ... tctggtttagCTCCGTGGTCGAAGTGGAAGACAGGGGGATCCTGGAAGCTCTCGCTTCTTTCTTAGTCTCGAGGATAATATTTTCCGGATCTTTGGAGGTGACAGGATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatact ... tctggtttagCTCCGTGGTCGAAGTGGAAGACAGGGGGATCCTGGAAGCTCTCGCTTCTTTCTTAGTCTCGAGGATAATATTTTCCGGATCTTTGGAGGTGACAGGATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatact ... tctggtttagCTCCGTGGTCGAAGTGGAAGACAGGGGGATCCTGGAAGCTCTCGCTTCTTTCTTAGTCTCGAGGATAATATTTTCCGGATCTTTGGAGGTGACAGGATAC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 113

GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAGgtaatatact ... tctggtttagCTCCGTGGTCGAAGTGGAAGACAGGGGGATCCTGGAAGCTCTCGCTTCTTTCTTAGTCTCGAGGATAATATTTTCCGGATCTTTGGAGGTGACAGGATAC