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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGGAAGAAAACTCATCCTGAATGTGCTCGATTTTCACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgctttctattgtacatttgcatgccaactccattgatatagcttggcttaagttctctaaattttcag

Basic information

species Zea mays
transcript GRMZM2G037683_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037683_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 5'ss of exon 6
TTTGGGAAGAAAACTCATCCTGAATGTGCTCGATTTTCACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgctttctattgtacatttgcatgccaactccattgatatagcttggcttaagttct--ctaaattttcag
|| |||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||| |||||||| ||||| ||||||  ||||| | | |   | |||| | ||  ||  || || || ||||||| || ||      ||| ||||||
TTCGGGAAGAAAACTCACCCTGAATGTGCTCGATTTTCACCTGATGGCCAGTACCTTGTATCATGCTCAGTGGATGGAATCATTGAGgtaagtctctttcaagtctgt-tctgcaggtcagttcttttaatgtaacttggctgaaatttcactaaaactttcag

upper sequence: GRMZM2G037683_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G30430.2 (Glycine max), 5'ss of exon 7
TTTGGGAAGAAAACTCATCCTGAATGTGCTCGATTTTCACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgctttctattgtacatttgcatgccaactccattgatatagcttggcttaagttctctaaattttcag
|||||||  |||| |||| | ||||||||| | |||||||| ||||| ||||  ||||| |||||||||||||||||  | ||||| |||   | | |   |||| |  ||    |  ||  | ||    | |   |     |   ||    | ||||  ||
TTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAGgta---tacata--attggagtttaaagtttcattttcagcagttttcttcctgattttttggacatatttctag

upper sequence: GRMZM2G037683_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G13560.2 (Glycine max), 5'ss of exon 7
TTTGGGAAGAAAACTCATCCTGAATGTGCTCGATTTTCACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgctttctattgtacatttgcatgc-caactccattgatatagcttggcttaagttctctaaattttcag
|||||||  |||| |||| | ||||||||| | |||||||| ||||| ||||  ||||| |||||||||||||||||  | ||||| |||       ||  | |  | | || |||   || ||   ||  |    | ||  ||   ||    | || |  ||
TTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAGgtatacatagttggacttaaaagtttcattttcagctgttttctt----cctgatttt--ttggacatatatctag

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|211525027|gb|FL310982.1|FL310982
EST:     GTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA                         GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATRTCAAGCC
genomic: GTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
EST: gi|211475898|gb|FL358552.1|FL358552
EST:     GTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA                         GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
genomic: GTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
EST: gi|76010783|gb|DT937953.1|DT937953
EST:     CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA                         GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCTATATCAAGCC
genomic: CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
EST: gi|67019283|gb|CO448032.1|CO448032
EST:     CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA                         GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
genomic: CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
EST: gi|23357683|gb|BU645332.1|BU645332
EST:     CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA                         GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
genomic: CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
EST: gi|111433444|gb|EE297761.1|EE297761
EST:     ACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA                         GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
genomic: ACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
EST: gi|22521028|gb|BU079839.1|BU079839
EST:     CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA                         GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
genomic: CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
EST: gi|211160334|gb|FL327726.1|FL327726
EST:     CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA                         GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
genomic: CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
EST: gi|26457208|gb|CA828791.1|CA828791
EST:     ACCTGATGGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA                         GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
genomic: ACCTGAT-GGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
EST: gi|91873183|gb|EB403140.1|EB403140
EST:     CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA                         GTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC
genomic: CACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCC

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: 214

TTTGGGAAGAAAACTCATCCTGAATGTGCTCGATTTTCACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

TTTGGGAAGAAAACTCATCCTGAATGTGCTCGATTTTCACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 95

TTTGGGAAGAAAACTCATCCTGAATGTGCTCGATTTTCACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58

TTTGGGAAGAAAACTCATCCTGAATGTGCTCGATTTTCACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgct ... aaattttcagGTCTGGGATTATCTTAGTGGAAAGCTTAAAAAGGATCTTCAATATCAAGCCGAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGGAAGAAAACTCATCCTGAATGTGCTCGATTTTCACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAAgtaagttgctttctattgtacatttgcatgccaactccattgatatagcttggcttaagttctctaaattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA