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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTTAAGGGGTCTTAACGTGTCTCTTTCGACTGACGACCCTCTACAAATTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccctatctctatctctgtcatgtgttttcccaatcccacccagaggttcttagtctggattgcttgttgctcttggcag

Basic information

species Zea mays
transcript GRMZM2G134396_T03
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 5'ss of exon 17
TTTCTTAAGGGGTCTTAACGTGTCTCTTTCGACTGACGACCCTCTACAAATTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaa-tgcccctatctctatctctgtcatgtgttttcccaatcccacccagaggttcttagtctggattgcttgttgctcttggcag
|||| |||| || |||||||| ||||| || || || |||||| | |||||||||||||| || |||||||||||||||||||| ||  | |||||||| |||| |  | |  || || |  || |   |   | |    || ||||  |||  | |||| | |||||||| |||   |||||||||
TTTCCTAAGAGGCCTTAACGTTTCTCTATCAACCGATGACCCTTTGCAAATTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatctccttcactctagctctttggatatgtttagattccacttagatctgcttaatttggattgcctgtcattcttggcag

upper sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 16
lower sequence: EFJ17267 (Selaginella moellendorffii), 5'ss of exon 15
TTTCTTAAGGGGTCTTAACGTGTCTCTTTCGACTGACGACCCTCTACAAATTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccctatctctatctctgtcatgtgttttcccaatcccacccagaggttcttagtctggattgcttgttgctcttggcag
|||     | || || || || || || ||||| || ||||||||||| || || || || ||||||||||||||||||||||||||| |||| |||   ||  | |   | | | |   | ||   |||  |  | ||   | | ||||       | |                          
TTTTGCTCGCGGGCTGAATGTTTCACTGTCGACGGATGACCCTCTACAGATCCATCTTACTAAGGAACCTTTGGTTGAAGAATACAGTATTGCAGCTCAGgttttactggtttttgttcttttgat-tgtaataactcag--ctaaccagtaccatctcgcag-----------------------

upper sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 16
lower sequence: EFJ30909 (Selaginella moellendorffii), 5'ss of exon 15
TTTCTTAAGGGGTCTTAACGTGTCTCTTTCGACTGACGACCCTCTACAAATTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccctatctctatctctgtcatgtgttttcccaatcccacccagaggttcttagtctggattgcttgttgctcttggcag
|||     | || || || || || || ||||| || ||||||||||| || || || || ||||||||||||||||||||||||||| |||| |||   ||  |     | | | |   | ||   |||  |  | ||   | | ||||       | |                          
TTTTGCTCGCGGGCTGAATGTTTCACTGTCGACGGATGACCCTCTACAGATACATCTTACTAAGGAACCTTTGGTTGAAGAATACAGTATTGCGGCTCAGgttttattggtttttgttcttttgat-tgtaataactcag--ctaaccagtaccatctcgcag-----------------------

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|14203330|gb|BG837007.1|BG837007
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|67028452|gb|CO457201.1|CO457201
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|78026552|gb|DV494939.1|DV494939
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|50336749|gb|CO531875.1|CO531875
EST:     CTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTT
genomic: CTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|74237693|gb|DT645607.1|DT645607
EST:     CCCCTGACGAAGGAACCTTTTGGT-GAAGAATACAGTGTTGCTGCCTTCC                         CTTTGGAAGCT
genomic: CACCTGACGAAGGAACCTTT-GGTTGAAGAATACAGTGTTGCTGC-TTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCT
EST: gi|71299097|gb|DR785545.1|DR785545
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|149090162|gb|EE179462.2|EE179462
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|211424036|gb|FL301688.1|FL301688
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|33090962|gb|CF050956.1|CF050956
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|71299098|gb|DR785546.1|DR785546
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|32931798|gb|CF036610.1|CF036610
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|78121620|gb|DV540004.1|DV540004
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|211281929|gb|FL464725.1|FL464725
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|4885898|gb|AI677018.1|AI677018
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|211424040|gb|FL301692.1|FL301692
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
EST: gi|71772852|gb|DR970775.1|DR970775
EST:     TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCA                         CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC
genomic: TTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTC

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: 47 (upstream exon), 49 (downstream exon)
Score: 207

TTTCTTAAGGGGTCTTAACGTGTCTCTTTCGACTGACGACCCTCTACAAATTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

TTTCTTAAGGGGTCTTAACGTGTCTCTTTCGACTGACGACCCTCTACAAATTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 406

TTTCTTAAGGGGTCTTAACGTGTCTCTTTCGACTGACGACCCTCTACAAATTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 151

TTTCTTAAGGGGTCTTAACGTGTCTCTTTCGACTGACGACCCTCTACAAATTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccc ... ctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCTTAAGGGGTCTTAACGTGTCTCTTTCGACTGACGACCCTCTACAAATTCACCTGACGAAGGAACCTTTGGTTGAAGAATACAGTGTTGCTGCTTCAgtaatgcccctatctctatctctgtcatgtgttttcccaatcccacccagaggttcttagtctggattgcttgttgctcttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT