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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtcatgaaactgacagccagcgtcacccctcctctcctgaacaattcacctatatacactgcctagtgactctgactgcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACTGGTCGTGCAGCGGCGTCTGTAAGTCGGTGGACCGGATGCGCCACATCCA

Basic information

species Zea mays
transcript GRMZM2G119265_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119265_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g65590.1 (Oryza sativa), 3'ss of exon 8
----------------------gtgggtcatgaaactgacagccagcgtcacccctcctctcctgaacaattca--cctatatacactgcctagtgactctgactgcgtgt-------gcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACTGGTCGTGCAGCGGCGTCTGTAAGTCGGTGGACCGGATGCGCCACATCCA
                       |   | || |   |   ||| || |  ||  ||||    | |||   ||||    | | |    ||  | |    |      || | |       ||||| |||||||||||||||||||| |||||||||||||||||||| ||||| ||||||||||| || ||||| ||||| |||||| |||||   ||||||||
gtcaatctcagctatcgattcttttcatgatcatcttcctagctagtggtactactccagatcagaatttttcagggttttttgttttgttttgaactttctttcgcatttttcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATTGGTCGTGCAGTGGGGTCTGCAAGTCAGTGGACAGGATGAAGCACATCCA

upper sequence: GRMZM2G119265_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G36830.1 (Glycine max), 3'ss of exon 7
gtgggtcatgaaactgacagccagcgtcacccctcctctcctgaacaattcacctatatacactgcc-tagtgactctgactgcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACTGGTCGTGCAGCGGCGTCTGTAAGTCGGTGGACCGGATGCGCCACATCCA
||  ||  |     ||  ||    | ||         |    ||| | |  |   ||||| | |  | |  |     ||  ||     ||||| || || ||||||    |  | || || ||||||||||| || || || ||||||||||| ||  ||||||||||||||||  | ||| |  | || ||
gtacgttttct--ttgctagttcacatc-ttatagagcgtacgaatattataaaaatatataatttcatttttgtcttgtttgtacacgcagATTGTGATTGGAAGGCAAGGACAGGAAATGTGTGCGTGGCATCTTTTGATTGGTCGTGCAGTGGTATCTGTAAGTCGGTGGAGAGAATGAGAGATATACA

upper sequence: GRMZM2G119265_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA12G00530.1 (Glycine max), 3'ss of exon 7
---------------------gtgggtcatgaaactgacagccagcgtcacccctcctctcctgaacaattcacctatatacactgcctag-tgactctgactgcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACTGGTCGTGCAGCGGCGTCTGTAAGTCGGTGGACCGGATGCGCCACATCCA
                         || ||  | |  ||    |   | |         || |    ||   |  | || |||||    |  | | |     ||      |||| || || ||||||    |  | || || ||||||||||| |||||||||||||| ||||| ||  ||||||||||||| ||  | ||| |  | || ||
gtacgttttctttgctagttcacatgttatagagcgtacgaatatttttatgtaagtattctttttaaaagaaattgta-acactataaaaataatttcatttgtacacacagATTGTGATTGGAAGGCAAGGACGGGAAATGTGTGCGTGGCATCCTTCGACTGGTCATGCAGTGGTATCTGTAAGTCGGTAGAGAGAATGAGAGATATACA

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|211502937|gb|FL440630.1|FL440630
EST:     CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|148946206|gb|EC891501.2|EC891501
EST:     CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|148982796|gb|EE028625.2|EE028625
EST:     CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|211315131|gb|FL268904.1|FL268904
EST:     CGAGGTCGAGCACGTCGACGACCGGAGCATGT-STGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|94472474|gb|EB701432.1|EB701432
EST:     CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|149105464|gb|EE290981.2|EE290981
EST:     CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|149009309|gb|EE153896.2|EE153896
EST:     CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|211026936|gb|FL261353.1|FL261353
EST:     CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|101401735|gb|EB822520.1|EB822520
EST:     CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|148954646|gb|EC900093.2|EC900093
EST:     GGAGGTGGAGCACGTCGACGACCGGAGCATGTGTTGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCTTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|148930010|gb|EE285878.2|EE285878
EST:     CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|149206024|gb|ES701620.1|ES701620
EST:     CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: CGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
EST: gi|211096514|gb|FL457294.1|FL457294
EST:     TGCGCGACGCCTCCAG                         ACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT
genomic: TGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACT

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 1 RNA-Seqlibrary.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 305

CACAGGTTCGCGAACGAGGACGTCTCGCTGGGGGCGTGGCTGATCGGGCTCGAGGTCGAGCACGTCGACGACCGGAGCATGTGCTGCGCGACGCCTCCAGgtgggtcatg ... gcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACTGGTCGTGCAGCGGCGTCTGTAAGTCGGTGGACCGGATGCGCCACATCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcctgaacaattcacctatatacactgcctagtgactctgactgcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACTGGTCGTGCAGCGGCGTCTGTAAGTCGGTGGACCGGATGCGCCACATCCA
                                     ctctgac  putative branch site (score: 305)
                  tatataca  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtcatgaaactgacagccagcgtcacccctcctctcctgaacaattcacctatatacactgcctagtgactctgactgcgtgtgcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACTGGTCGTGCAGCGGCGTCTGTAAGTCGGTGGACCGGATGCGCCACATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA