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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgcttgctcctttctgttttattttttacgtgcagcatctagttatgtgtgtctattaggaaaactaaagagagcattcgctgttcctgcacata...

Basic information

species Zea mays
transcript GRMZM5G825902_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825902_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 5'ss of exon 4
ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgcttgctcctttctgttttattttttacgtgcagcatctagttatgtgtgtctattaggaaaactaaagagagcattcgctgttcctgcacata-----
||||| |||||||||||||| ||||||||||| || |||||||||||| ||||||| ||||||||||||||||||||||||||||||||||||| ||||||||  ||  |||||||| |  |   ||  ||    |||   |||  || | | | | | | | |     |       ||  ||   |  || ||      
ATGAAGGCACTCAAGGACCTGGGCCTTGATGTGACGAAAGGAAGTGTGTCAACTGAATCAGCTGTCACACAAACAAAGTTCCACATCATGCGATCgtgggtgcacgccactttctgtgtgctgcattttgt----catgctgtttagtttatatttgaagtagag-ggtgtattttctcattgaatccacatatttatca
















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|6020732|gb|AW065540.1|AW065540
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACAT
EST: gi|31351917|gb|CD436274.1|CD436274
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|213192723|gb|FM191866.1|FM191866
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|26558566|gb|CA830801.1|CA830801
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|67035504|gb|CO464037.1|CO464037
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|5325248|gb|AI783439.1|AI783439
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACA
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACA
EST: gi|31355619|gb|CD439976.1|CD439976
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|31353042|gb|CD437399.1|CD437399
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCNTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|211133671|gb|FL369481.1|FL369481
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|149100918|gb|EE187014.2|EE187014
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|87157787|gb|DY402576.1|DY402576
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|8516597|gb|BE123322.1|BE123322
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|5847192|gb|AW000271.1|AW000271
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|5325091|gb|AI783282.1|AI783282
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|22545865|gb|BU098239.1|BU098239
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|149074678|gb|EE163096.2|EE163096
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|71447368|gb|DR828418.1|DR828418
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|6526657|gb|AW215948.1|AW215948
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|148999647|gb|EE036634.2|EE036634
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|6194493|gb|AW146597.1|AW146597
EST:     ACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: ACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|31363719|gb|CD448076.1|CD448076
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|5871295|gb|AW017766.1|AW017766
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|5860476|gb|AW011698.1|AW011698
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|5871459|gb|AW017930.1|AW017930
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
EST: gi|211502811|gb|FL321803.1|FL321803
EST:     GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT                         TGGGCGCAAGGTTGAGGACCCTGACATG
genomic: GTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATG

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: 205

ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 625

ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 298

ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgctt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATTgtgggtgcttgctcctttctgttttattttttacgtgcagcatctagttatgtgtgtctattaggaaaactaaagagagcattcgctgttcctgcacata

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaactaa