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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcaccttttctgtttcacacattttttcctctttctgcttgttgatagtgtgttctggcctttttggggtgtaaattttattttgtctggtcaag

Basic information

species Zea mays
transcript GRMZM2G157462_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 11
GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcaccttttctgtttcacacattttttcctctt--tctgcttgttgatagtgt--gttctggcctttttggggtgtaaattttat-tttgtctggtcaag
|| |||||||||||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||   || ||| | |  || |||||| |     | |  |||| ||| ||   || | | ||  |  | ||  ||| | ||| |||   |   ||||
GTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAGgtatcacctag-ctattttagagtttctttcctttcgagtttcacgttggtagagtttattgttgactgatgtgagtaaaaaatctatgtttcctttcgcaag

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcaccttttctgtttcacacattttttcctctttctgcttgttgatagtgtgttctggcctttttggggtgtaaattttattttgtctggtcaag
||||| || ||  |  | ||||||||    |||||||| ||||||||||| || ||||||||||||||||| || ||| | ||||||       || |  | | |      || | | ||||  |||  | ||||    ||||   |||        || ||                    
GTTCACCGAGTGCTTGTTGACATAGTTTCAGCTTCCGCGAATGCCACACCTGGTCTTGGGAGATATCCTCCTTTTAAGAGAGAGgtaattatgcttttactgctctttcagttgcatttttcgtcttactaatagctgtttcttttcttaaataatcgtcaaccag----------------

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacc--ttttctgtttcacacattttttcctctttctgcttgttgatagtgtgttctggcctttttggggtgtaaattttattttgtctggtcaag
||||| || ||  |  | ||||||||    ||||| |||||||| ||||| |||||||||||||||||||| |||||||| ||||||  |    |||| || | |    |||   |  | |||   | | | | ||     |  |  ||||| ||     |||   | |    |          
GTTCACCGAGTTCTTGTTGACATAGTTTCAGCTTCTGCAAATGCTACACCTGGACTTGGGAGATATCCTCCTTTCAAGCGAGAGgtaataatgattttttggtgc-tttattcagtaatattttatcatttcggtaacagttatt--cctttctgac---taatcatcaaccag----------

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|211286766|gb|FK982432.1|FK982432
EST:     CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG                         GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST: gi|9254689|gb|BE345157.1|BE345157
EST:     CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG                         GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST: gi|211286763|gb|FK982429.1|FK982429
EST:     CCGCAAATGCCACACCGGGACTTGGGAGATATCCTCCATTCAAGCGTGAG                         GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST: gi|87155357|gb|DY400146.1|DY400146
EST:     CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG                         GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST: gi|30306992|gb|CD001665.1|CD001665
EST:     CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG                         GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST: gi|211132359|gb|FK982426.1|FK982426
EST:     CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG                         GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST: gi|31361304|gb|CD445661.1|CD445661
EST:     CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG                         GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTGGAGAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST: gi|31354322|gb|CD438679.1|CD438679
EST:     CCGCAAATGCCATACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG                         GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 330

GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 406

GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 425

GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 261

GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcaccttttctgtttcacacattttttcctctttctgcttgttgatagtgtgttctggcctttttggggtgtaaattttattttgtctggtcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT