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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctcaaatgaagagtgaaattagttgctttgtttacaggtattgctgtggatatttaaaacttgaacgtactttgatacttgaaccacaaaacatgcag

Basic information

species Zea mays
transcript GRMZM5G871262_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871262_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctc--------aaatgaagagtgaaatta--gttgctttgttta------caggtat-----tgctgtggatatt------taaaact--tgaacgtactttgatacttgaaccacaaaacatgcag
|||||||||| |||||||| |||||||| ||||||||||| ||||| |||||||||||||||||| ||||||| || ||||||||||||||||| |||||||  || ||        ||||  | ||| |  |||  |||| ||  |  |        | |||     ||  |||||||||      | |||||  ||||  |  | ||||  || |||  |  || ||||||
TCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAGTATCTCTACAAgtatgtatctagcatgcaaatccatagtcagtttacagttgtttgctcgaataagctggatatatccatgtggtggatattggagcatcaaacttttgaaaatgttctgat--tttaacatctgaatatgcag

upper sequence: GRMZM5G871262_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G18160.1 (Glycine max), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctcaaatgaagagtgaaattagttgctttgtttacaggtattgctgtggatatttaaaacttgaacgtactttgatacttgaaccacaaaacatgcag-
||||  |||| || |||||||| ||||| ||||||||||| || || || || ||||||||||| ||| | || ||||| |||||||| ||| | ||||||||||||   |||   || |     |   |   ||| |      |  | ||| ||  |   |         | |  |   |   |  |     | | ||  ||  
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAATATTTGTACAAgtgagtc---aatcgggatttcttctgcctctcttgctc-tgccttatactg-gggcaaaaatggtcccttccttttgctaagttgtagatctagagcacacaat

upper sequence: GRMZM5G871262_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA03G07890.1 (Glycine max), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctcaaatgaagagtgaaattagttgctttgtttacaggtattgctg--tggatatttaaaactt-gaacgtactttgatacttgaaccacaaaacatgcag
||||  |||| || |||||||| ||||| ||||||||||| || || || || ||||||||||| ||| | || |||||||||||||| ||| | ||||||| ||||  |  || | | |    |   |  || |    |    | |   ||  || | || | ||   | |||| ||   |  |  || |    ||||   |    
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtca-agctggatattt--ttccctcactctccccaaccctctgattgggtgaagatgtgaagtatagaacctaaacttttcgtttacttgcaaattgt----

upper sequence: GRMZM5G871262_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA16G19230.1 (Glycine max), 5'ss of exon 11
TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctcaaatgaagagtgaaattagttgctttgtttacaggtattgctgtggatatttaaaacttgaacgtactttgatacttgaaccacaaaacatgcag-
||||  |||| || |||||||| ||||| ||||||||||| || || || || ||||||||||| ||| | || ||||| |||||||| ||| | ||||||||||||   |||   || |     |   |   ||| |      |  | ||| ||  |   |         | |  |   |   |  |     | | ||  ||  
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAATATTTGTACAAgtgagtc---aatctggatttcttctgcctctcttgctc-tgccttatactg-gggcaaaaatggtcccttccttttgctaagttgtagatctagagcacacaat

upper sequence: GRMZM5G871262_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA01G30400.1 (Glycine max), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctcaaatgaagagtgaaattagttgctttgtttacaggt--attgctgtggatatttaaaactt-gaacgtactttgatacttgaaccacaaaacatgcag
||||  |||| || |||||||| ||||| ||||||||||| || || || || ||||||||||| ||| |||| |||||||||||||| ||| | ||||||| ||||  |  || | | |           |||     ||   |  ||||  ||| | |  | ||   | |||| |||  |  |  || |    ||||        
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtca-agctggatatttttcccgcgctcttccccaacccttggattgg-gtgaagacgtgaagtatagaacctacacttttcgttaacttgcaaattt-----

upper sequence: GRMZM5G871262_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G43020.1 (Glycine max), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctcaaatgaagagtgaaattagt-tgctttgtttacaggtattgctgtggatatttaaaacttgaacgtactttgatacttgaaccacaaaacatgcag
||||  |||| || |||||||| ||||| ||||||||||| || || || || ||||| ||||| ||| | || ||||| |||||||| ||| | ||||||||||||      ||    |     |    |||| ||  | | |||   ||        |       ||  ||    ||  | |  |  | |||| ||       
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAATATTTGTACAAgtgagtcagtctggattcttctgcctctcctgctctgccttctggtggggcaaaaatggtcccttcttttcactatgttgtaaatctagagcacacaatg-----

upper sequence: GRMZM5G871262_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctcaaatgaagagtgaaattagttgctttgtttacaggtattg--ctgtggatatttaaaacttgaacgtactttgatacttgaaccacaaaacatgcag
|||| ||||| || ||||  |||||||| ||||| || || ||||| ||||| ||||||||||| ||||| |||||||| || |||||||| || ||||||| |||   |   |     || || ||   |  |   ||      ||    |||  |||| |     |||   | ||     ||  || |                
TCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAGTACCTCTACAAgtaagtaatatcgggtttttgcaaataaaggtctcacttgtgtacataagactgatgataatcttcccttt--cttatcggtatctttcag---------------

upper sequence: GRMZM5G871262_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctcaaatgaagagtgaaat-tagttgctttgtttacaggtattgctgtggatatttaaaacttgaacgtactttgatacttgaaccacaaaacatgcag
| |||||||| || ||||  ||||| || ||||| |||||||| || ||||| ||||||||||||||||| |||||| | ||||||||||| |||||||||| |||   | | |  |  | | || |||  |   | |          || || |  |  || |   ||     || ||                          
TTTGTGCCACTGCATTTGGATATTACGCTCAAGCCACTGCTGCCCAGGAGATATTTGGCCACACATTGCAGTCCCTTAGAGGAATTAAGTACCTTTACAAgtaagt---agaagtggtataacatatagcagtcatatgctatatccgtgatgcgtcttattgaggttt---tatatttcag-----------------------

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|78121981|gb|DV540365.1|DV540365
EST:     ATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTT
genomic: ATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctca ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTT
EST: gi|89251977|gb|DY623763.1|DY623763
EST:     ATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTT
genomic: ATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctca ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTT

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), 47 (downstream exon)
Score: 255

TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctca ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 205

TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctca ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 317

TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctca ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 274

TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctca ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTT